8ROS | pdb_00008ros

human pyridoxine 5-phosphate oxidase in complex with Z isomer of pyridoxilidenrhodanine 5-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NRG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	12% PEG 6000, 0.1 lithium sulfate, 0.1 sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.15	α = 90
b = 83.15	β = 90
c = 59.17	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	100	PIXEL	DECTRIS PILATUS 6M		2021-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.553	45.758	100	1	24.9	18.3		34420

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.553	1.58			0.803

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	THROUGHOUT	1.553	45.758	34420	1675	99.962	0.165	0.1627	0.1722	0.2004	0.2066	27.431

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]
-0.499	-0.25		-0.499		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.651
r_dihedral_angle_other_3_deg	24.047
r_dihedral_angle_4_deg	17.921
r_dihedral_angle_3_deg	12.877
r_lrange_it	6.831
r_lrange_other	6.787
r_dihedral_angle_1_deg	6.689
r_scangle_it	5.551
r_scangle_other	5.549
r_scbond_it	3.756
r_scbond_other	3.754
r_mcangle_it	3.066
r_mcangle_other	3.066
r_mcbond_it	2.232
r_mcbond_other	2.227
r_angle_refined_deg	1.768
r_angle_other_deg	1.435
r_xyhbond_nbd_refined	0.219
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.196
r_symmetry_nbd_other	0.19
r_nbd_other	0.186
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.147
r_chiral_restr	0.098
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1714
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing