1VKO

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	0.12M Na Cl, 0.90M Tartrate_K Na, 0.084M Imidazole, 0.016M Imidazole Chloride , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.04
2.78	55.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.98	α = 90
b = 129.98	β = 90
c = 131.32	γ = 90

Symmetry
Space Group	I 2 2 2

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 315	FLAT MIRROR	2002-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1

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	2.3	29.41	98	0.059	14.5	3.9		28995			49.54

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	2.3	2.42	98.6		0.344	3.9	3.9	4221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Obtained from MAD data of a crystal of SE-MET substituted protein in space group P21 21 2	2.3	29.41	27525	1470	97.55	0.20352	0.20035	0.26455	RANDOM	32.35

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]
4.39			1.05		-5.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.468
r_dihedral_angle_3_deg	17.577
r_dihedral_angle_4_deg	16.642
r_scangle_it	8.73
r_dihedral_angle_1_deg	6.944
r_scbond_it	6.732
r_mcangle_it	3.433
r_mcbond_it	1.976
r_angle_refined_deg	1.608
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.468
r_dihedral_angle_3_deg	17.577
r_dihedral_angle_4_deg	16.642
r_scangle_it	8.73
r_dihedral_angle_1_deg	6.944
r_scbond_it	6.732
r_mcangle_it	3.433
r_mcbond_it	1.976
r_angle_refined_deg	1.608
r_nbtor_refined	0.312
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.165
r_metal_ion_refined	0.152
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4007
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	58

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling
MOLREP	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 R01GM133198.