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ZP-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in P21221)
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 2.8 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.34 α = 90 b = 92.16 β = 90 c = 140.95 γ = 90
Symmetry Space Group P 21 2 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 MARRESEARCH 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) CC (Half) 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 2.05 50 99.9 0.106 0.999 13.09 7.43 75254 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 99.9 0.3863 0.188 0.67 7.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 3D4C 2.05 32.898 1.33 75143 1857 99.83 0.2099 0.2091 0.2103 0.2411 0.2409 RANDOM 66
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.553 f_angle_d 0.783 f_chiral_restr 0.046 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7291 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing PHENIX refinement