2ZRZ | pdb_00002zrz

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced 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	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.879	α = 90
b = 100.879	β = 90
c = 334.864	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	2.9	50	99.6	0.09	22.1	11.9		39430			63.6

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	2.9	3	96.9		0.412	2.5	6.1

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	2.9	48.85	37374	1970	99.49	0.19318	0.19212	0.19	0.2129	0.21	RANDOM	45.543

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.368
r_dihedral_angle_4_deg	23.408
r_dihedral_angle_3_deg	19.83
r_dihedral_angle_1_deg	5.53
r_scangle_it	2.561
r_angle_refined_deg	1.572
r_scbond_it	1.449
r_mcangle_it	1.265
r_mcbond_it	0.734
r_symmetry_vdw_refined	0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.368
r_dihedral_angle_4_deg	23.408
r_dihedral_angle_3_deg	19.83
r_dihedral_angle_1_deg	5.53
r_scangle_it	2.561
r_angle_refined_deg	1.572
r_scbond_it	1.449
r_mcangle_it	1.265
r_mcbond_it	0.734
r_symmetry_vdw_refined	0.344
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.212
r_chiral_restr	0.177
r_xyhbond_nbd_refined	0.151
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	172
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.