2VNP

Monoclinic form of IDI-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HX3PDB ENTRY 1HX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2544.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.2α = 90
b = 69.1β = 100.3
c = 62.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.23097.80.0617.52.5181194
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.495.60.169

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HX32.1936.21742694197.60.1970.1940.255RANDOM23.91
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]
0.010.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.794
r_dihedral_angle_4_deg19.483
r_dihedral_angle_3_deg16.114
r_dihedral_angle_1_deg7.472
r_scangle_it4.026
r_scbond_it2.91
r_angle_refined_deg2.092
r_mcangle_it1.775
r_mcbond_it1.175
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.794
r_dihedral_angle_4_deg19.483
r_dihedral_angle_3_deg16.114
r_dihedral_angle_1_deg7.472
r_scangle_it4.026
r_scbond_it2.91
r_angle_refined_deg2.092
r_mcangle_it1.775
r_mcbond_it1.175
r_nbtor_refined0.307
r_nbd_refined0.229
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.226
r_xyhbond_nbd_refined0.157
r_chiral_restr0.146
r_bond_refined_d0.026
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2821
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing