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Sucrose phosphorylase from Jeotgalibaca ciconiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Protein was concentrated to 16 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 25% PEG 3350, 0.1 M Bis-tris propane, pH 6.5, 50 mM Na/K phosphate
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.639 α = 90 b = 90.828 β = 92.832 c = 96.17 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 PILATUS3 2M 2021-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 2.05 48 98.8 0.123 0.172 0.121 0.987 5.9 3 54973
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 2.05 2.11 0.908 1.269 0.885 0.336 2.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QQI 2.05 48 54948 2719 98.669 0.199 0.1958 0.1957 0.2544 0.2555 31.144
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] 0.944 0.442 -0.56 -0.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_1_deg 7.14 r_lrange_it 6.462 r_lrange_other 6.45 r_scangle_it 4.99 r_scangle_other 4.99 r_mcangle_it 3.68 r_mcangle_other 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_1_deg 7.14 r_lrange_it 6.462 r_lrange_other 6.45 r_scangle_it 4.99 r_scangle_other 4.99 r_mcangle_it 3.68 r_mcangle_other 3.68 r_scbond_it 3.251 r_scbond_other 3.25 r_mcbond_other 2.591 r_mcbond_it 2.59 r_angle_refined_deg 1.571 r_angle_other_deg 1.28 r_nbd_other 0.243 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.171 r_ncsr_local_group_1 0.106 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7846 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 8
Software Software Software Name Purpose XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement