5F5S

Crystal structure of the Prp38-MFAP1 complex of Homo sapiens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RZ9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.4277.150.1 M sodium acetate, pH 4.4 and 15% (v/v) 1,3-Butandiol
Crystal Properties
Matthews coefficientSolvent content
2.5150.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.79α = 90
b = 66.79β = 90
c = 242.54γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.21.24BESSY14.2

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
12.457.841000.07224.618.513389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.461001.919.3

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 REPLACEMENTFREE R-VALUE4rz92.457.841270868199.90.22330.22140.2609RANDOM94.494
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]
1.190.591.19-3.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.016
r_dihedral_angle_3_deg17.54
r_dihedral_angle_4_deg17.217
r_dihedral_angle_1_deg4.588
r_scbond_it4.249
r_mcangle_it4.236
r_mcbond_it2.636
r_angle_refined_deg0.972
r_chiral_restr0.068
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.016
r_dihedral_angle_3_deg17.54
r_dihedral_angle_4_deg17.217
r_dihedral_angle_1_deg4.588
r_scbond_it4.249
r_mcangle_it4.236
r_mcbond_it2.636
r_angle_refined_deg0.972
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1930
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction