7QAR | pdb_00007qar

Serial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.6	291	TRIS-ACETATE, PEG 8000, MUA,

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.79	α = 90
b = 96.03	β = 90
c = 105.21	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS3 6M		2019-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03	PETRA III, DESY	P11

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	2.3	17.07	99.98	0.849	0.3668	2.44	28.2		18280

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100		0.225	1.9369	0.52	20.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4CW2	2.3	17.07	18280	919	99.64	0.221	0.2182	0.22	0.2661	0.27	36.703

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]
1.332			-0.446		-0.886

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.473
r_dihedral_angle_3_deg	14.087
r_dihedral_angle_4_deg	13.027
r_dihedral_angle_1_deg	6.931
r_lrange_it	4.195
r_lrange_other	4.194
r_mcangle_other	2.81
r_mcangle_it	2.809
r_scangle_it	2.67
r_scangle_other	2.67
r_mcbond_it	1.612
r_mcbond_other	1.611
r_scbond_it	1.522
r_scbond_other	1.522
r_angle_other_deg	1.438
r_angle_refined_deg	1.388
r_nbd_other	0.207
r_nbd_refined	0.203
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.123
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_ext_dist_refined_d	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2359
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing