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Crystal structure of ubch5c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QCQ PDB ENTRY 1QCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2 38.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.998 α = 90 b = 44.334 β = 93.36 c = 97.584 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 Bruker DIP-6040 2004-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 1.8 100 93.9 0.04 20.9 2.8 46077 21.7
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) 1.8 1.86 83.8 0.249
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QCQ 1.85 20 46077 41012 2178 94.68 0.20376 0.20376 0.19949 0.28222 0.2978 RANDOM 28.5
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] 0.61 0.57 -0.55 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.404 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 17.039 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.763 r_scbond_it 2.538 r_mcangle_it 1.611 r_angle_refined_deg 1.467 r_mcbond_it 0.993 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.404 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 17.039 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.763 r_scbond_it 2.538 r_mcangle_it 1.611 r_angle_refined_deg 1.467 r_mcbond_it 0.993 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.225 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4867 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing