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Crystal structure of a Human VH domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ModelArchive MA-CNZ8J ENTRY 1HOU that was moved from PDB to ModelArchive
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir solution 100mM MES, pH6.5, 10mM ZnSO4, 25% v/v PEG550MME, 4mM DTT and 0.04% v/v NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.92 35.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.336 α = 90 b = 37.965 β = 109.67 c = 37.187 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH Rh coated mirror 2003-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.802 EMBL/DESY, HAMBURG X31
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 1.5 34.922 90.7 0.047 27.69 4.29 15017 16.67
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) 1.5 1.53 92.9 0.214 7.26 4.1 696
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1HOU 1.5 20 15144 14358 762 99.89 0.1763 0.15979 0.15787 0.1629 0.19652 0.1927 RANDOM 21.603
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] -0.75 -0.54 1.87 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.651 r_scangle_it 3.897 r_scbond_it 3.504 r_mcangle_it 3.229 r_mcbond_it 1.924 r_angle_refined_deg 1.735 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.651 r_scangle_it 3.897 r_scbond_it 3.504 r_mcangle_it 3.229 r_mcbond_it 1.924 r_angle_refined_deg 1.735 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 877 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing