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ADP Complex OF HUMAN PAPS SYNTHETASE 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X6V PDB ENTRY 1X6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 290 1 mM ADP was soaked into native crystals (PDB ENTRY 1X6V) for one hour, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.5 α = 90 b = 82.5 β = 105 c = 133 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 CCD ADSC QUANTUM 4 2003-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 20 97.5 0.104 0.083 13.6 7.4 100470
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 2.05 2.1 89.5 0.609 0.741 2.48 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 WITH INITIAL MERCURY PHASES THROUGHOUT PDB ENTRY 1X6V 2.06 129.1 100470 92501 4869 96.56 0.17383 0.17135 0.1807 0.22147 0.23 RANDOM 37.726
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] 1.6 1.22 0.77 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.54 r_scangle_it 3.694 r_mcangle_it 3.549 r_angle_refined_deg 2.474 r_scbond_it 2.411 r_mcbond_it 2.303 r_angle_other_deg 1.319 r_symmetry_hbond_refined 0.287 r_nbd_other 0.283 r_symmetry_vdw_other 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.54 r_scangle_it 3.694 r_mcangle_it 3.549 r_angle_refined_deg 2.474 r_scbond_it 2.411 r_mcbond_it 2.303 r_angle_other_deg 1.319 r_symmetry_hbond_refined 0.287 r_nbd_other 0.283 r_symmetry_vdw_other 0.249 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.235 r_symmetry_vdw_refined 0.2 r_chiral_restr 0.162 r_nbtor_other 0.107 r_bond_refined_d 0.034 r_bond_other_d 0.029 r_gen_planes_other 0.018 r_gen_planes_refined 0.016 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9206 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 81
Software Software Software Name Purpose X-GEN data scaling XDS data reduction XFIT data reduction REFMAC refinement X-GEN data reduction XDS data scaling