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Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Null
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.57 α = 90 b = 146.57 β = 90 c = 222.227 γ = 90
Symmetry Space Group P 41 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 PILATUS3 6M 2016-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9800 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.82 73.29 100 0.119 0.126 0.041 0.999 12.7 9 215182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 100 1.992 2.108 0.68 0.407 9.2
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 FOURIER SYNTHESIS THROUGHOUT 6GGY 1.82 73.29 204179 10878 99.92 0.1952 0.194 0.1989 0.2185 0.2235 RANDOM 39.822
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] 0.5 0.5 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 14.382 r_dihedral_angle_3_deg 12.523 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.4 r_angle_other_deg 0.957 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 14.382 r_dihedral_angle_3_deg 12.523 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.4 r_angle_other_deg 0.957 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13931 Nucleic Acid Atoms Solvent Atoms 720 Heterogen Atoms 94
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing