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Human GMP synthetase in complex with XMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YWC PDB ENTRY 2YWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 0.1M NAAC,PH 5.2,1.6M AMSO4, 0.2M NACL
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.52 α = 90 b = 123.42 β = 90 c = 127.96 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD MIRRORS 2008-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 20 99.7 0.09 19 7.7 54472 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 100 0.587 4.12 7.8
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 (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 PDB ENTRY 2YWC 2.5 19.92 51746 2724 100 0.206 0.203 0.2029 0.256 0.2561 RANDOM 36.38
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] 0.37 0.64 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.048 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 5.568 r_scangle_it 3.698 r_scbond_it 2.178 r_mcangle_it 1.679 r_angle_refined_deg 1.203 r_mcbond_it 0.863 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.048 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 5.568 r_scangle_it 3.698 r_scbond_it 2.178 r_mcangle_it 1.679 r_angle_refined_deg 1.203 r_mcbond_it 0.863 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other 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 10019 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing