3S8I

The retroviral-like protease (RVP) domain of human DDI1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629121% PEG3350, 0.2 M AMMONIUM PHOSPHATE, 0.1 M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1542.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.981α = 90
b = 41.04β = 107.62
c = 88.975γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC MIRRORS2011-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.73097.80.04352.3726.93025430254-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7373.40.3147.745.31112

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 DIFFRACTIONMRTHROUGHOUTpdb entry 2ILA1.728.2728725149997.650.176860.175730.19871RANDOM27.812
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]
-0.42-0.590.65-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.323
r_dihedral_angle_4_deg17.444
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg6.303
r_scangle_it3.645
r_scbond_it2.473
r_angle_refined_deg1.457
r_mcangle_it1.338
r_mcbond_it0.757
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.323
r_dihedral_angle_4_deg17.444
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg6.303
r_scangle_it3.645
r_scbond_it2.473
r_angle_refined_deg1.457
r_mcangle_it1.338
r_mcbond_it0.757
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1891
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms27

Software

Software
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling