3QKB | pdb_00003qkb

Crystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	30.00% MPD, 0.200M NH4OAc, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.296	α = 90
b = 67.301	β = 90
c = 85.836	γ = 90

Symmetry
Space Group	P 21 21 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)	2009-07-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162,0.97929	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	2.73	47.727	98.8	0.1	10.92			17422		-3	60.247

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	2.73	2.83	99.3		0.757	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	MAD	THROUGHOUT	2.73	47.727	17408	884	98.95	0.2037	0.2018	0.1961	0.2393	0.2265	RANDOM	54.0681

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]
-0.48			-0.27		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.195
r_dihedral_angle_3_deg	15.258
r_dihedral_angle_1_deg	7.727
r_scangle_it	2.355
r_scbond_it	1.492
r_angle_refined_deg	1.295
r_mcangle_it	1.151
r_angle_other_deg	1.107
r_mcbond_it	0.605
r_mcbond_other	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.195
r_dihedral_angle_3_deg	15.258
r_dihedral_angle_1_deg	7.727
r_scangle_it	2.355
r_scbond_it	1.492
r_angle_refined_deg	1.295
r_mcangle_it	1.151
r_angle_other_deg	1.107
r_mcbond_it	0.605
r_mcbond_other	0.102
r_chiral_restr	0.069
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3543
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
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.