3K2K | pdb_00003k2k

Crystal structure of putative carboxypeptidase (YP_103406.1) from BURKHOLDERIA MALLEI ATCC 23344 at 2.49 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	4.3000M NaCl, 0.1M HEPES pH 7.5, Additive: 0.006 M calcium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.375	α = 90
b = 162.375	β = 90
c = 148.397	γ = 90

Symmetry
Space Group	I 41 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror, vertical and horizontal focussing mirrors	2009-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.49	29.553	99.1	0.076	15.45			34624		-3	61.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.58	92		0.78	2.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.49	29.553	34608	1742	99.51	0.157	0.156	0.16	0.185	0.19	RANDOM	36.226

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]
-1.18			-1.18		2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.612
r_dihedral_angle_4_deg	20.219
r_dihedral_angle_3_deg	14.463
r_scangle_it	7.866
r_scbond_it	5.993
r_dihedral_angle_1_deg	5.018
r_mcangle_it	3.355
r_mcbond_it	1.86
r_angle_refined_deg	1.563
r_angle_other_deg	0.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.612
r_dihedral_angle_4_deg	20.219
r_dihedral_angle_3_deg	14.463
r_scangle_it	7.866
r_scbond_it	5.993
r_dihedral_angle_1_deg	5.018
r_mcangle_it	3.355
r_mcbond_it	1.86
r_angle_refined_deg	1.563
r_angle_other_deg	0.905
r_mcbond_other	0.432
r_chiral_restr	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3052
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.