7ZS8 | pdb_00007zs8

Mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae at 1.4 Angstrom resolution

X-RAY DIFFRACTION

---

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		278	0.1 M MES pH 6.0, 30 % 5/4 PO/OH, 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN

Crystal Properties
Matthews coefficient	Solvent content
2.1	43.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.842	α = 90
b = 89.144	β = 90
c = 89.731	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	PIXEL	DECTRIS PILATUS 2M-F		2016-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.4	39.95	99.9	0.068	0.999	11.4	6.4		124619

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42			0.0656	0.813

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	1.4	39.95	118011	6220	99.6	0.19763	0.19638	0.21	0.22096	0.23	RANDOM	18.815

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]
-0.22			-1.55		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.305
r_dihedral_angle_4_deg	19.409
r_dihedral_angle_3_deg	11.688
r_dihedral_angle_1_deg	5.726
r_long_range_B_refined	4.92
r_long_range_B_other	4.864
r_scangle_other	4.261
r_scbond_other	3.028
r_scbond_it	3.027
r_mcangle_it	2.322
r_mcangle_other	2.322
r_angle_refined_deg	1.972
r_mcbond_it	1.784
r_mcbond_other	1.781
r_angle_other_deg	1.193
r_chiral_restr	0.126
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5050
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	176

Software

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