7VCE

Structural studies of human inositol monophosphatase-1 inhibition by ebselen

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AS4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292.15	0.2 M magnesium formate and 20% (wt/vol) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 75.72	β = 95.6
c = 57.51	γ = 90

Symmetry
Space Group	P 1 21 1

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		2013-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	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	2.6	45.04	98.75	0.993	8.57	1.8		14825

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	2.6	2.693			0.733

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4AS4	2.6	45.04	14825	764	98.78	0.23	0.2006	0.2436	37.693

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]
1.162		-2.299	0.626		-1.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.411
r_dihedral_angle_3_deg	15.181
r_dihedral_angle_4_deg	12.867
r_dihedral_angle_1_deg	5.012
r_lrange_it	4.222
r_lrange_other	4.168
r_mcangle_other	2.78
r_mcangle_it	2.763
r_scangle_other	2.695
r_scangle_it	2.684
r_angle_other_deg	1.893
r_scbond_other	1.743
r_mcbond_other	1.714
r_scbond_it	1.703
r_mcbond_it	1.679
r_angle_refined_deg	1.169
r_symmetry_xyhbond_nbd_refined	0.379
r_xyhbond_nbd_refined	0.294
r_nbd_other	0.242
r_symmetry_nbd_other	0.201
r_nbd_refined	0.186
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.158
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.06
r_bond_other_d	0.055
r_dihedral_angle_other_3_deg	0.034
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3707
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing