3EWM | pdb_00003ewm

Crystal structure of an uncharacterized sugar kinase PH1459 from pyrococcus horikoshii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	18% PEG 8000; 0.2M calcium acetate; 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.757	α = 90
b = 79.373	β = 94.18
c = 82.99	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	ADSC QUANTUM 210	mirrors	2008-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9795	NSLS	X12C

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	57.26	99.2	0.145	12	7.2	44270	44270

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)
	1.9	2	95.3		0.307	3.9	6	6148

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	1.9	57.26	44270	42006	2262	99.1	0.19217	0.18969	0.19	0.23906	0.24	RANDOM	19.528

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]
0.21		-0.26	0.24		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.272
r_dihedral_angle_4_deg	21.743
r_dihedral_angle_3_deg	15.807
r_dihedral_angle_1_deg	5.605
r_scangle_it	3.439
r_scbond_it	2.203
r_mcangle_it	1.353
r_angle_refined_deg	1.3
r_mcbond_it	0.905
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.272
r_dihedral_angle_4_deg	21.743
r_dihedral_angle_3_deg	15.807
r_dihedral_angle_1_deg	5.605
r_scangle_it	3.439
r_scbond_it	2.203
r_mcangle_it	1.353
r_angle_refined_deg	1.3
r_mcbond_it	0.905
r_nbtor_refined	0.309
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4584
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
SHELX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	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.