2ZRY | pdb_00002zry

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	30% PEG 400, 0.2M sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.359	α = 90
b = 100.359	β = 90
c = 334.607	γ = 90

Symmetry
Space Group	P 43 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	95	CCD	ADSC QUANTUM 270	mirror	2008-06-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000, 1.13980, 1.14022, 1.04000	Photon Factory	BL-17A

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	2.64	50	93.6	0.09	18.9	8.8		48278			52.8

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	2.64	2.74	68.2		0.338	2.2	4.4

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	2.64	49.63	45809	2450	93.59	0.18474	0.18271	0.18	0.22254	0.22	RANDOM	42.393

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.17
r_dihedral_angle_4_deg	21.901
r_dihedral_angle_3_deg	19.511
r_dihedral_angle_1_deg	5.827
r_scangle_it	3.138
r_scbond_it	1.87
r_angle_refined_deg	1.541
r_mcangle_it	1.187
r_mcbond_it	0.697
r_symmetry_hbond_refined	0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.17
r_dihedral_angle_4_deg	21.901
r_dihedral_angle_3_deg	19.511
r_dihedral_angle_1_deg	5.827
r_scangle_it	3.138
r_scbond_it	1.87
r_angle_refined_deg	1.541
r_mcangle_it	1.187
r_mcbond_it	0.697
r_symmetry_hbond_refined	0.358
r_symmetry_vdw_refined	0.324
r_nbtor_refined	0.312
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.123
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11232
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	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.