3PFO | pdb_00003pfo

Crystal structure of a putative acetylornithine deacetylase (RPA2325) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	277	0.2M NH4Formate, 20.0% PEG-3350, No Buffer pH 6.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.074	α = 90
b = 48.823	β = 111.02
c = 111.879	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	CCD	MARMOSAIC 325 mm CCD		2010-01-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97927,0.97913	SSRL	BL9-2

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	1.9	29.584	95.9	0.048	11.39	2.94		68415		-3	24.705

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	1.9	1.97	94.4		0.492	1.76

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	MAD	THROUGHOUT	1.9	29.584	68322	3437	98	0.1731	0.1714	0.18	0.2042	0.21	RANDOM	38.3193

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]
0.38		0.4	0.98		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.604
r_dihedral_angle_4_deg	19.063
r_dihedral_angle_3_deg	12.452
r_dihedral_angle_1_deg	6.215
r_scangle_it	3.252
r_scbond_it	2.028
r_angle_refined_deg	1.418
r_mcangle_it	1.155
r_angle_other_deg	0.909
r_mcbond_it	0.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.604
r_dihedral_angle_4_deg	19.063
r_dihedral_angle_3_deg	12.452
r_dihedral_angle_1_deg	6.215
r_scangle_it	3.252
r_scbond_it	2.028
r_angle_refined_deg	1.418
r_mcangle_it	1.155
r_angle_other_deg	0.909
r_mcbond_it	0.646
r_mcbond_other	0.194
r_chiral_restr	0.087
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	6431
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
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.