2PHC | pdb_00002phc

Crystal structure of conserved uncharacterized protein PH0987 from Pyrococcus horikoshii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	289	USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.23 mg/mL) IN 20mM Tris-HCl pH 8.0, 1mM DTT, AND SOLUTION CONTAINING 17.5% w/v PEG 3350, 0.2 M Na Iodide, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.848	α = 90
b = 105.848	β = 90
c = 51.869	γ = 120

Symmetry
Space Group	P 61

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 300 mm CCD	ROSENBAUM	2007-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97243	APS	22-ID

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	2.29	50	100	0.057	28.1	15		15078

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	2.29	2.38	100		0.322		13.8	1499

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	2.29	18.33	15018	761	99.97	0.242	0.239	0.24	0.294	0.26	RANDOM	33.324

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]
0.06	0.03		0.06		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.365
r_dihedral_angle_1_deg	22.808
r_dihedral_angle_3_deg	17.98
r_dihedral_angle_4_deg	15.381
r_scangle_it	5.551
r_scbond_it	4.092
r_angle_refined_deg	2.581
r_mcangle_it	2.343
r_mcbond_it	2.102
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.365
r_dihedral_angle_1_deg	22.808
r_dihedral_angle_3_deg	17.98
r_dihedral_angle_4_deg	15.381
r_scangle_it	5.551
r_scbond_it	4.092
r_angle_refined_deg	2.581
r_mcangle_it	2.343
r_mcbond_it	2.102
r_nbtor_refined	0.328
r_xyhbond_nbd_refined	0.306
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.245
r_chiral_restr	0.232
r_symmetry_vdw_refined	0.226
r_bond_refined_d	0.03
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1690
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction

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.