4KMW | pdb_00004kmw

Structure of the Y34N MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A FROM AMPHITRITE ORNATA WITH 2,4,6-TRICHLOROPHENOL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	28-32% PEG4K, .2M ammonium sulfate, .02M sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.553	α = 90
b = 67.259	β = 90
c = 67.89	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2012-03-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.79	50	99	0.079	9.7	5.4	25994	25737	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.82	91		0.501		4	1166

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.79	47.78	33356	25678	1299	98.94	0.218	0.1499	0.1457	0.16	0.2322	0.24	RANDOM	28.62

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]
0.6			-0.66		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.098
r_dihedral_angle_2_deg	36.008
r_dihedral_angle_4_deg	22.295
r_sphericity_bonded	17.906
r_dihedral_angle_3_deg	13.295
r_rigid_bond_restr	5.761
r_mcangle_it	5.301
r_dihedral_angle_1_deg	5.055
r_mcbond_it	4.44
r_mcbond_other	4.436

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.098
r_dihedral_angle_2_deg	36.008
r_dihedral_angle_4_deg	22.295
r_sphericity_bonded	17.906
r_dihedral_angle_3_deg	13.295
r_rigid_bond_restr	5.761
r_mcangle_it	5.301
r_dihedral_angle_1_deg	5.055
r_mcbond_it	4.44
r_mcbond_other	4.436
r_angle_refined_deg	1.589
r_angle_other_deg	1.153
r_chiral_restr	0.137
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_other_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2130
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	112

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

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.