6FU3 | pdb_00006fu3

Structure of the mixed-valence, active 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	2VHD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	278	30% 5/4 PO/OH and 0.1M MES pH6.0 in the presence of 2mM CaCl2, 10mM sodium ascorbate and 0.2mM FMN, using a 20mg/mL protein solution previously incubated with calcium, sodium ascorbate and FMN.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.942	α = 90
b = 88.78	β = 90
c = 93.122	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	CMOS	BRUKER PHOTON 100		2016-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.5418

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	64.3	99.1	0.1565	10.3	9.2		61589

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			0.8398

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	2VHD	1.8	23.82	57511	2997	98.71	0.20946	0.20769	0.22	0.2436	0.25	RANDOM	21.856

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.62
r_dihedral_angle_4_deg	16.007
r_dihedral_angle_3_deg	13.663
r_dihedral_angle_1_deg	6.167
r_long_range_B_refined	6.167
r_long_range_B_other	6.114
r_scangle_other	4.905
r_scbond_it	3.667
r_scbond_other	3.663
r_mcangle_it	2.76
r_mcangle_other	2.76
r_angle_refined_deg	2.198
r_mcbond_other	2.119
r_mcbond_it	2.118
r_angle_other_deg	1.228
r_chiral_restr	0.139
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5062
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	174

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM	data reduction
SAINT	data scaling
PHASER	phasing