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Crystal structure of the Prp38-MFAP1 complex of Homo sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.4 277.15 0.1 M sodium acetate, pH 4.4 and 15% (v/v) 1,3-Butandiol
Crystal Properties Matthews coefficient Solvent content 2.51 50.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.79 α = 90 b = 66.79 β = 90 c = 242.54 γ = 120
Symmetry Space Group P 61 2 2
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 RAYONIX MX-225 2013-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.24 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.4 57.84 100 0.072 24.6 18.5 13389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 100 1.9 19.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4rz9 2.4 57.84 12708 681 99.9 0.2233 0.2214 0.2194 0.2609 0.2596 RANDOM 94.494
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] 1.19 0.59 1.19 -3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.016 r_dihedral_angle_3_deg 17.54 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_1_deg 4.588 r_scbond_it 4.249 r_mcangle_it 4.236 r_mcbond_it 2.636 r_angle_refined_deg 0.972 r_chiral_restr 0.068 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.016 r_dihedral_angle_3_deg 17.54 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_1_deg 4.588 r_scbond_it 4.249 r_mcangle_it 4.236 r_mcbond_it 2.636 r_angle_refined_deg 0.972 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1930 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction