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Crystal Structure of The Human MDC1 FHA Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UMZ PDB ENTRY 3UMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 3350, 0.1M HEPES (pH 7.5), 50mM KCl, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.651 α = 90 b = 56.053 β = 97.53 c = 64.92 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 MARMOSAIC 225 mm CCD 2009-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9796 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 20 97.7 0.079 13 3.4 20009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 91.2 0.448 2.3 917
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 THROUGHOUT PDB ENTRY 3UMZ 1.8 20 19821 1027 97.65 0.2365 0.2344 0.2353 0.2741 0.278 RANDOM 31.1747
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] 0.58 0.23 1.24 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.856 r_dihedral_angle_4_deg 16.15 r_dihedral_angle_3_deg 15.154 r_dihedral_angle_1_deg 5.736 r_scangle_it 3.618 r_scbond_it 2.105 r_mcangle_it 1.618 r_angle_refined_deg 1.241 r_mcbond_it 0.854 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.856 r_dihedral_angle_4_deg 16.15 r_dihedral_angle_3_deg 15.154 r_dihedral_angle_1_deg 5.736 r_scangle_it 3.618 r_scbond_it 2.105 r_mcangle_it 1.618 r_angle_refined_deg 1.241 r_mcbond_it 0.854 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1623 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction