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P. patens sedoheptulose-1,7-bisphosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 281 40 % PEG 600
0.2 M imidazole/malate
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.18 α = 90 b = 70.417 β = 90 c = 197.245 γ = 90
Symmetry Space Group P 2 2 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 PIXEL DECTRIS PILATUS 6M 2015-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0001 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 100 99.3 0.067 0.998 30.6 10.7 155382 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 MOLECULAR REPLACEMENT THROUGHOUT 1D9Q 1.3 98.62 122301 6340 82.68 0.1612 0.15969 0.159 0.1908 0.19 RANDOM 19.237
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] -0.08 0.06 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.464 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 14.28 r_long_range_B_refined 6.971 r_long_range_B_other 6.971 r_dihedral_angle_1_deg 6.747 r_scangle_other 4.954 r_scbond_it 3.195 r_scbond_other 3.183 r_mcangle_other 2.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.464 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 14.28 r_long_range_B_refined 6.971 r_long_range_B_other 6.971 r_dihedral_angle_1_deg 6.747 r_scangle_other 4.954 r_scbond_it 3.195 r_scbond_other 3.183 r_mcangle_other 2.833 r_mcangle_it 2.832 r_angle_refined_deg 2.317 r_mcbond_it 1.81 r_mcbond_other 1.807 r_angle_other_deg 0.985 r_chiral_restr 0.147 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4863 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing