4UAT | pdb_00004uat

Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form I

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	25 % PEG-550MME, 0.1 M MES-NaOH pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.419	α = 90
b = 51.468	β = 94.06
c = 122.083	γ = 90

Symmetry
Space Group	P 1 21 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 2M		2013-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.97639	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	121.776	99.5	0.066	0.074	0.033	13.2	4.7	107256	107256

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.37	97.4		0.839	0.839	0.451	0.9	4.2	15268

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	PDB entry 4UAR	1.3	30	107186	5342	99.43	0.1235	0.1212	0.12	0.1685	0.17	RANDOM	16.916

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]
1.07		-0.2	-0.26		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.806
r_dihedral_angle_2_deg	30.413
r_dihedral_angle_4_deg	19.755
r_dihedral_angle_3_deg	13.018
r_sphericity_bonded	11.348
r_dihedral_angle_1_deg	6.244
r_rigid_bond_restr	6.034
r_angle_refined_deg	2.049
r_angle_other_deg	0.955
r_chiral_restr	0.249

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.806
r_dihedral_angle_2_deg	30.413
r_dihedral_angle_4_deg	19.755
r_dihedral_angle_3_deg	13.018
r_sphericity_bonded	11.348
r_dihedral_angle_1_deg	6.244
r_rigid_bond_restr	6.034
r_angle_refined_deg	2.049
r_angle_other_deg	0.955
r_chiral_restr	0.249
r_bond_refined_d	0.021
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	3466
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	62

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
XSCALE	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.