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Crystal structure of human synaptonemal complex protein SYCP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD SOLUTION OF THE IODIDE DERVIATIVE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS CRYSTALLISED FROM 100 MM HEPES PH 7.5, 100 MM NACL, 13.0% (W/V) PEG3350; THEN SOAKED IN 20% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.87 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.14 α = 66.53 b = 92.381 β = 82.32 c = 103.367 γ = 76.53
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M MIRRORS 2012-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.24 47.36 86.7 0.15 11 9.7 66412 35.48
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 2.24 2.29 38.9 1.09 2.5 8.1
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 SAD SOLUTION OF THE IODIDE DERVIATIVE STRUCTURE 2.24 47.36 66411 3301 85.26 0.1968 0.1953 0.204 0.2262 0.2341 RANDOM 61.34
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] 10.017 -4.6158 -4.3874 -40.8688 -14.2862 30.8518
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.98 t_omega_torsion 2.1 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.98 t_omega_torsion 2.1 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9810 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX phasing BUSTER-TNT phasing BUSTER refinement