3CIN | pdb_00003cin

CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN (TM_1419) FROM THERMOTOGA MARITIMA MSB8 AT 1.70 A RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GR0	PDB entry 1GR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	NANODROP, 0.2M MgCl2, 40.0% PEG 400, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.304	α = 90
b = 104.95	β = 90
c = 117.013	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 210	KOHZU: Double Crystal Si(111)	2003-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000	ALS	8.2.1

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	1.7	41.135	93.2	0.05	21.9	2.9		43592			23.939

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	1.7	1.73	72.6		0.455	2.1	2.2	2238

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1GR0	1.7	41.135	43592	2181	92.68	0.161	0.16	0.17	0.194	0.17	RANDOM	27.035

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]
-1.06			2.65		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_4_deg	17.122
r_dihedral_angle_3_deg	14.116
r_scangle_it	7.257
r_dihedral_angle_1_deg	5.78
r_scbond_it	5.256
r_mcangle_it	3.261
r_mcbond_it	2.552
r_angle_refined_deg	1.711
r_angle_other_deg	0.998
r_mcbond_other	0.669
r_symmetry_vdw_refined	0.333
r_symmetry_vdw_other	0.284
r_nbd_refined	0.22
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.112
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2956
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
MOLREP	phasing