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Active dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPZ PDB entry 1GPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 288 14% (w/v) PEG 6000, 0.2 M NaCl, 10% (v/v) glycerol, 0.1 M Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.07 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.541 α = 90 b = 92.416 β = 90 c = 162.848 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm mirror 2002-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 2.6 54.981 99.7 0.089 6.1 6.7 35308 35308 68.122
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 2.6 2.67 98.9 0.489 1.5 6.3 2466
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 1GPZ 2.6 54.31 33537 33537 1768 100 0.21306 0.21306 0.2106 0.2175 0.25938 0.2629 RANDOM 20.399
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] 0.11 -0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 15.702 r_dihedral_angle_1_deg 7.353 r_mcangle_it 1.784 r_angle_refined_deg 1.498 r_angle_other_deg 1.366 r_scangle_it 1.308 r_mcbond_it 1.215 r_scbond_it 0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 15.702 r_dihedral_angle_1_deg 7.353 r_mcangle_it 1.784 r_angle_refined_deg 1.498 r_angle_other_deg 1.366 r_scangle_it 1.308 r_mcbond_it 1.215 r_scbond_it 0.865 r_symmetry_vdw_other 0.306 r_nbd_other 0.207 r_mcbond_other 0.201 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_other 0.121 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6079 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling BEAST phasing