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Crystal Structure Analysis of LaPhzM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWZ pdbid 3gwz
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M ammonium formate, 18 - 22 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.275 α = 90 b = 81.017 β = 98.23 c = 72.164 γ = 90
Symmetry Space Group P 1 21 1
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 2017-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.42 71.421 97.1 0.041 15.3 3.4 117067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 98 0.441 0.441 1.8 3.4
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 PDBID 3GWZ 1.42 71.42 111168 5873 97 0.182 0.181 0.1813 0.203 0.2038 RANDOM 18.57
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] -0.2 -0.22 0.29 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 5.539 r_angle_refined_deg 1.517 r_angle_other_deg 0.76 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_dihedral_angle_4_deg 18.566 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 5.539 r_angle_refined_deg 1.517 r_angle_other_deg 0.76 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5092 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction