9KP8 | pdb_00009kp8

Crystal structure of FAD-dependent oxidase CpaO

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.245	α = 90
b = 118.245	β = 90
c = 68.891	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER X 9M		2022-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.179	30	98.96	0.038	58.19	9		178136

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.179	1.22			0.431	0.148	0.941	5.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.179	24.246	178136	8926	98.959	0.164	0.1635	0.1733	0.1736	0.1865	14.425

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]
0.001			0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.726
r_dihedral_angle_3_deg	11.781
r_dihedral_angle_1_deg	6.246
r_lrange_it	5.593
r_lrange_other	5.161
r_dihedral_angle_2_deg	4.949
r_scangle_other	1.66
r_scangle_it	1.657
r_scbond_other	1.037
r_scbond_it	1.036
r_angle_refined_deg	1.017
r_mcangle_it	0.953
r_mcangle_other	0.953
r_angle_other_deg	0.602
r_mcbond_it	0.595
r_mcbond_other	0.594
r_symmetry_nbd_refined	0.31
r_nbd_refined	0.264
r_symmetry_nbd_other	0.248
r_nbd_other	0.247
r_dihedral_angle_other_2_deg	0.219
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.13
r_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.05
r_gen_planes_refined	0.013
r_gen_planes_other	0.011
r_bond_refined_d	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	697
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALA	data scaling
MOLREP	phasing
HKL-2000	data reduction