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Human Cyclophilin D in complex with norbornane fragment derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 50 mM potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.889 α = 90 b = 56.889 β = 90 c = 116.147 γ = 90
Symmetry Space Group P 43 21 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 PIXEL DECTRIS PILATUS 6M 2013-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 SLS X06SA
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 51.09 95.8 0.113 11.01 4.5 12987 24.48
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) 1 2 2.25 97.5 0.514 3.04 4.5
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 4J5B 2 40.23 12985 1283 95.8 0.195 0.192 0.1942 0.226 0.2328 RANDOM 25.72
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] 2.8231 2.8231 -5.6463
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.39 t_omega_torsion 6.18 t_angle_deg 1.15 t_bond_d 0.011 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 13.39 t_omega_torsion 6.18 t_angle_deg 1.15 t_bond_d 0.011 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 1236 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 64
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling MOLREP phasing