3BS4 | pdb_00003bs4

Crystal structure of uncharacterized protein PH0321 from Pyrococcus horikoshii in complex with an unknown peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	100mM Tri-sodium citrate dihydrate pH 7.0, 20% PEG 4000, 20% Isopropanol, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.241	α = 90
b = 71.121	β = 93.01
c = 49.581	γ = 90

Symmetry
Space Group	C 1 2 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	MAR CCD 165 mm		2007-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	57.378	97.17	0.095	0.095	13.5	7.6	43226	43226			19.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	96.5		0.669	0.669	2.8	7.5	6216

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.6	20	43223	43223	2179	97.17	0.185	0.184	0.19	0.208	0.21	RANDOM	24.401

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]
0.65		0.81	0.02		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	17.266
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	11.217
r_scangle_it	3.813
r_scbond_it	2.411
r_mcangle_it	1.457
r_angle_refined_deg	1.287
r_mcbond_it	0.895
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	17.266
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	11.217
r_scangle_it	3.813
r_scbond_it	2.411
r_mcangle_it	1.457
r_angle_refined_deg	1.287
r_mcbond_it	0.895
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.11
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.