2ZRX | pdb_00002zrx

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

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
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.071	α = 90
b = 101.071	β = 90
c = 333.43	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	2008-03-05	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	3	50	95.9	0.092	13.2	4.5		34495			64.4

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	3	3.11	90.9		0.092	2.1	3.7

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	3	45.22	32758	1713	96.06	0.18564	0.18407	0.18	0.21473	0.21	RANDOM	47.268

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	37.559
r_dihedral_angle_4_deg	21.791
r_dihedral_angle_3_deg	19.659
r_dihedral_angle_1_deg	5.758
r_scangle_it	2.255
r_angle_refined_deg	1.472
r_scbond_it	1.288
r_mcangle_it	1.024
r_mcbond_it	0.568
r_symmetry_vdw_refined	0.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.559
r_dihedral_angle_4_deg	21.791
r_dihedral_angle_3_deg	19.659
r_dihedral_angle_1_deg	5.758
r_scangle_it	2.255
r_angle_refined_deg	1.472
r_scbond_it	1.288
r_mcangle_it	1.024
r_mcbond_it	0.568
r_symmetry_vdw_refined	0.331
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.268
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.116
r_metal_ion_refined	0.02
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11232
Nucleic Acid Atoms
Solvent Atoms	175
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.