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Structures of MECP synthase in complex with (i) CMP and (ii) CMP and product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GX1 PDB ENTRY 1GX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 10-20% PEG 2000 MONOETHYL ETHER, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.082 α = 90 b = 117.582 β = 90.21 c = 54.215 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 2002-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 30 95.8 0.05 13.2 1.8 141167 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 2.07 91 0.38 2 1.8
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 1GX1 1.99 87.71 69794 3708 97.9 0.216 0.214 0.2077 0.252 0.2389 RANDOM 31.34
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] -1.83 -0.33 4.25 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.588 r_scangle_it 4.336 r_scbond_it 2.639 r_mcangle_it 1.81 r_angle_refined_deg 1.625 r_mcbond_it 0.994 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.281 r_nbd_other 0.253 r_symmetry_vdw_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.588 r_scangle_it 4.336 r_scbond_it 2.639 r_mcangle_it 1.81 r_angle_refined_deg 1.625 r_mcbond_it 0.994 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.281 r_nbd_other 0.253 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.139 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.1 r_metal_ion_refined 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.003 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_other 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 6974 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing