7KOS | pdb_00007kos

1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KOM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: Classics II (C3), 2.4M Sodium malonate pH 7.0 Cryo: 25% Sucrose, 1.2M Sodium malonate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.462	α = 90
b = 91.81	β = 90
c = 99.22	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	CCD	MARMOSAIC 300 mm CCD	Be	2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	1.5	30	99.9	0.046	0.046	0.051	0.021	31.3	5.8		118548		-3	21.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.796	0.796	0.875	0.361	0.82	2.4	5.8

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	7kom	1.5	29.04	111854	5910	99.85	0.1525	0.1515	0.1522	0.1723	0.1726	RANDOM	25.236

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]
-0.75			-0.93		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.877
r_dihedral_angle_4_deg	14.86
r_dihedral_angle_3_deg	10.249
r_dihedral_angle_1_deg	4.573
r_angle_refined_deg	1.435
r_angle_other_deg	0.402
r_chiral_restr	0.068
r_gen_planes_refined	0.055
r_gen_planes_other	0.051
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4581
Nucleic Acid Atoms
Solvent Atoms	736
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing