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Human kallikrein 7 in complex with 1,3,6-trisubstituted 1,4-diazepane-7-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG1000, PEG3350, 2-methyl-2,4-pentanediol, sodium nitrate, sodium hydrogen phosphate, ammonium sulfate, bicine/trizma buffer
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.895 α = 90 b = 90.926 β = 90 c = 92.03 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2010-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 100 87.8 11.4 5.2 12132
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 2QXI 2.15 33.68 11541 583 87.87 0.21138 0.20823 0.2112 0.27555 0.2791 RANDOM 23.168
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] -0.16 -0.3 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.964 r_dihedral_angle_4_deg 23.059 r_dihedral_angle_3_deg 19.118 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 4.088 r_long_range_B_other 4.075 r_scangle_other 2.617 r_mcangle_it 1.995 r_mcangle_other 1.995 r_angle_refined_deg 1.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.964 r_dihedral_angle_4_deg 23.059 r_dihedral_angle_3_deg 19.118 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 4.088 r_long_range_B_other 4.075 r_scangle_other 2.617 r_mcangle_it 1.995 r_mcangle_other 1.995 r_angle_refined_deg 1.773 r_scbond_it 1.68 r_scbond_other 1.663 r_mcbond_it 1.262 r_mcbond_other 1.26 r_angle_other_deg 1.058 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing