2AT8 | pdb_00002at8

0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) 2,4 Dimethyl Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8O	PDB entry 1X8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	300	ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

Crystal Properties
Matthews coefficient	Solvent content
1.59	22.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.211	α = 90
b = 42.582	β = 94.61
c = 52.935	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	Bent conical Si-mirror (Rh coating)	2005-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	0.96	21.29	86.4	0.08	0.08	22.6	3.16		81981			11.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	0.96	0.99	89	89	0.41	0.41	2.9	1.54	8392

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB entry 1X8O	1	21.29	72220	72220	3642	85.94	0.166	0.166	0.165	0.17	0.195	0.2	RANDOM	11.95

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.27		0.03	0.03		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.275
r_dihedral_angle_3_deg	12.042
r_dihedral_angle_4_deg	8.299
r_dihedral_angle_1_deg	7.313
r_scangle_it	4.385
r_scbond_it	3.396
r_mcangle_it	2.397
r_angle_refined_deg	1.747
r_mcbond_it	1.739
r_nbd_refined	0.418

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.275
r_dihedral_angle_3_deg	12.042
r_dihedral_angle_4_deg	8.299
r_dihedral_angle_1_deg	7.313
r_scangle_it	4.385
r_scbond_it	3.396
r_mcangle_it	2.397
r_angle_refined_deg	1.747
r_mcbond_it	1.739
r_nbd_refined	0.418
r_nbtor_refined	0.31
r_metal_ion_refined	0.28
r_symmetry_vdw_refined	0.266
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.116
r_xyhbond_nbd_refined	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1722
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	48

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.