☰ Navigation Tabs
ZP-N domain of mammalian sperm receptor ZP3 (crystal form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4C PDB ENTRY 3D4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M Tris-HCL, PH7.2, 0.001M maltose.
Reservoir: 10% PEG6000, 0.2M calcium chloride, 0.1M Tris-HCL, PH7.0.
Sample to reservoir ratio in drop: 1:1, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.05 α = 89.99 b = 91.96 β = 90.18 c = 140.48 γ = 89.98
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 2006-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95350 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 500 95.4 0.05 11 2 202456 193240 -3 48.357
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.35 95.7 0.529 1.6 2 12935
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 (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 3D4C 2.3 50 202438 193225 2139 95.45 0.2017 0.2014 0.2047 0.2265 0.2321 RANDOM 50.67
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] -1.23 -0.06 -0.65 0.97 -0.08 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_4_deg 14.974 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 5.525 r_angle_other_deg 4.207 r_scangle_it 1.353 r_angle_refined_deg 0.927 r_scbond_it 0.779 r_mcangle_it 0.778 r_mcbond_it 0.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_4_deg 14.974 r_dihedral_angle_3_deg 12.755 r_dihedral_angle_1_deg 5.525 r_angle_other_deg 4.207 r_scangle_it 1.353 r_angle_refined_deg 0.927 r_scbond_it 0.779 r_mcangle_it 0.778 r_mcbond_it 0.425 r_symmetry_vdw_other 0.264 r_nbd_other 0.217 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.177 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.139 r_nbtor_other 0.127 r_metal_ion_refined 0.117 r_chiral_restr 0.051 r_xyhbond_nbd_other 0.042 r_symmetry_metal_ion_refined 0.013 r_bond_refined_d 0.007 r_gen_planes_other 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29088 Nucleic Acid Atoms Solvent Atoms 1934 Heterogen Atoms 208
Software Software Software Name Purpose PHASER phasing REFMAC refinement MxCuBE data collection XDS data reduction XDS data scaling