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Crystal structure of pseudecin from Pseudechis porphyriacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 3.6M sodium formate, 10%(w/v) glycerol, 0.15M NaCl, 50mM Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.707 α = 90 b = 61.668 β = 90 c = 251.224 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.0000 Photon Factory BL-6B
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 1.9 50 98.5 0.109 4.7 6.2 74335 21.7
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 1.9 1.97 100 0.315 2.1 7.2 7454
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 (All) 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 1WVR 1.9 43.27 74329 3745 100 0.209 0.206 0.2063 0.258 0.257 RANDOM 26.737
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 r_dihedral_angle_2_deg 34.542 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.445 r_scbond_it 1.537 r_angle_refined_deg 1.173 r_mcangle_it 1.078 r_mcbond_it 0.581 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.542 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.445 r_scbond_it 1.537 r_angle_refined_deg 1.173 r_mcangle_it 1.078 r_mcbond_it 0.581 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.111 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6532 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing