6QKN | pdb_00006qkn

Structure of the azide-inhibited form of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FU3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	30 % 5/4 PO/OH and 0.1 M MES pH 6.0 in the presence of 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.12	α = 90
b = 89.14	β = 90
c = 94.83	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	110	PIXEL	DECTRIS PILATUS 2M		2016-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979	ESRF	BM30A

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	2.3	65	97.7	0.117	9.2	5.6		30270

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	2.3	2.38			0.723

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	6FU3	2.3	64.95	28748	1466	99.18	0.17336	0.1712	0.18	0.21461	0.22	RANDOM	39.118

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]
0.39			-1.5		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.888
r_dihedral_angle_4_deg	15.076
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_1_deg	6.05
r_long_range_B_refined	4.952
r_long_range_B_other	4.934
r_scangle_other	3.227
r_scbond_it	2.315
r_mcangle_it	2.304
r_mcangle_other	2.304
r_scbond_other	2.197
r_angle_refined_deg	1.907
r_mcbond_it	1.515
r_mcbond_other	1.501
r_angle_other_deg	1.106
r_chiral_restr	0.108
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5059
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	180

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing