7NWR | pdb_00007nwr

Structure of BT1526, a myo-inositol-1-phosphate synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QVT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	200 mM Sodium Formate 100 mM Bis Tris propane pH 6.5 20 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.805	α = 90
b = 104.563	β = 90
c = 124.318	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9796	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	58.85	100	0.998	11.2	13.3		59644

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.541		13.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3QVT	2	58.847	59567	2989	99.963	0.185	0.183	0.18	0.2252	0.23	34.103

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]
-0.185			0.145		0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.994
r_dihedral_angle_4_deg	19.07
r_dihedral_angle_3_deg	14.903
r_dihedral_angle_1_deg	6.39
r_lrange_it	6.167
r_scangle_it	5.078
r_scbond_it	3.667
r_mcangle_it	3.394
r_mcbond_it	2.541
r_angle_refined_deg	1.407
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.096
r_ncsr_local_group_1	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6738
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
xia2	data reduction
PHASER	phasing
Coot	model building