3NOL | pdb_00003nol

Crystal structure of Zymomonas mobilis Glutaminyl Cyclase (trigonal form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IWA	PDB ENTRY 2IWA

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.423	α = 90
b = 61.423	β = 90
c = 98.8	γ = 120

Symmetry
Space Group	P 31 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		IMAGE PLATE	RIGAKU RAXIS IV++	confocal	2007-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.7	53.225	99.9	0.086	0.086	21	8.4	24365	24365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.536	0.536	0.574	0.201	1.4	8	3510

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	PDB ENTRY 2IWA	1.7	22.46	24339	1241	99.91	0.1798	0.1777	0.18	0.2202	0.22	RANDOM	11.9369

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]
0.23	0.11		0.23		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.269
r_dihedral_angle_4_deg	15.66
r_dihedral_angle_3_deg	11.921
r_dihedral_angle_1_deg	6.936
r_scangle_it	2.878
r_scbond_it	1.895
r_angle_refined_deg	1.395
r_mcangle_it	1.17
r_mcbond_it	0.743
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.09
r_metal_ion_refined	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1897
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection