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Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XZP PDB ENTRY 1XZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM TRIS-HCl, pH 7.5, 22% (w/v) PEG 550 MME, 10mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 6.730611 81.725288
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.279 α = 90 b = 124.279 β = 90 c = 174.701 γ = 90
Symmetry Space Group P 43 21 2
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 MAR CCD 165 mm MIRRORS 2007-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.28186 SLS X10SA
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 3.2 20 99.4 0.127 0.178 8.61 7.8 23250 23100 76.546
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 3.2 3.3 99.9 0.485 2.18 8.03 2004
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 1XZP 3.2 19.99 21913 1186 99.91 0.24192 0.24053 0.2436 0.26743 0.2676 RANDOM 52.543
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] 1.09 1.09 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.203 r_dihedral_angle_3_deg 20.574 r_dihedral_angle_4_deg 16.015 r_dihedral_angle_1_deg 5.696 r_angle_refined_deg 1.185 r_scangle_it 0.919 r_mcangle_it 0.704 r_scbond_it 0.493 r_mcbond_it 0.388 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.203 r_dihedral_angle_3_deg 20.574 r_dihedral_angle_4_deg 16.015 r_dihedral_angle_1_deg 5.696 r_angle_refined_deg 1.185 r_scangle_it 0.919 r_mcangle_it 0.704 r_scbond_it 0.493 r_mcbond_it 0.388 r_nbtor_refined 0.295 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 3364 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling