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Crystal structure of the H101A mutant ecHint GMP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N1S PDB ENTRY 3N1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 40% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20mM Tris pH 7.0, 1 mM EDTA, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.327 α = 90 b = 64.066 β = 109.04 c = 74.75 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 113 CCD MARMOSAIC 325 mm CCD mirrors 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.975 SSRL BL9-1
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 1.716 37.7 88.2 0.08 3.4 41405 41372 2 2 31.6
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) 1.716 1.76 25.8 0.47 2.1
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 3N1S 1.716 35.33 39308 2075 87.65 0.19644 0.19387 0.2046 0.24543 0.2552 RANDOM 24.767
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] -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_4_deg 21.762 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 6.719 r_scangle_it 4.146 r_scbond_it 2.861 r_angle_refined_deg 2.029 r_mcangle_it 1.58 r_mcbond_it 1.034 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_4_deg 21.762 r_dihedral_angle_3_deg 17.799 r_dihedral_angle_1_deg 6.719 r_scangle_it 4.146 r_scbond_it 2.861 r_angle_refined_deg 2.029 r_mcangle_it 1.58 r_mcbond_it 1.034 r_nbtor_refined 0.314 r_nbd_refined 0.276 r_chiral_restr 0.244 r_symmetry_vdw_refined 0.209 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.183 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 3560 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling