3L2N | pdb_00003l2n

Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, ADDITIVE: CALCIUM CHLORIDE 0.006 M, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.417	α = 90
b = 81.417	β = 90
c = 479.685	γ = 120

Symmetry
Space Group	P 61 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 focusing)	2009-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.39	49.147	99.7	0.206	13.16			38954		-3	40.987

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	2.39	2.48	98.9		0.013	2.5

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	2.39	49.147	38841	1947	99.86	0.182	0.18	0.18	0.233	0.22	RANDOM	26.223

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]
2.15	1.07		2.15		-3.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.031
r_dihedral_angle_4_deg	17.026
r_dihedral_angle_3_deg	12.924
r_scangle_it	6.828
r_dihedral_angle_1_deg	5.281
r_scbond_it	5.263
r_mcangle_it	2.65
r_mcbond_it	1.558
r_angle_refined_deg	1.546
r_angle_other_deg	0.907

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.031
r_dihedral_angle_4_deg	17.026
r_dihedral_angle_3_deg	12.924
r_scangle_it	6.828
r_dihedral_angle_1_deg	5.281
r_scbond_it	5.263
r_mcangle_it	2.65
r_mcbond_it	1.558
r_angle_refined_deg	1.546
r_angle_other_deg	0.907
r_mcbond_other	0.516
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5891
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	24

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.