6YL7 | pdb_00006yl7

Crystal structure of beta carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	22% PEG 4000, 10% isopropanol, 100 mM HEPES pH 7.5 and 3% v/v 1,5-Diaminopentene di-HCl.

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.738	α = 90
b = 88.738	β = 90
c = 112.428	γ = 120

Symmetry
Space Group	P 64 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	100	PIXEL	DECTRIS PILATUS3 S 6M		2018-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0399	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.17	45.41	99.9	0.341	0.354	0.093	1	9.7	24.7		4883

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.17	3.38			2.96	3.08	0.84	1

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	4rxy	3.17	45.41	4605	208	99.46	0.197	0.1926	0.2	0.2962	0.3	RANDOM	90.296

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]
2.01	1		2.01		-6.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.684
r_dihedral_angle_3_deg	22.128
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_1_deg	8.946
r_angle_refined_deg	1.587
r_angle_other_deg	1.276
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.684
r_dihedral_angle_3_deg	22.128
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_1_deg	8.946
r_angle_refined_deg	1.587
r_angle_other_deg	1.276
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1548
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

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.