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CRYSTAL STRUCTURE OF ENOLASE BRADO_4202 (TARGET EFI-501651) FROM Bradyrhizobium sp. ORS278 WITH CALCIUM AND ACETATE BOUND
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDR PDB ENTRY 1MDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.1M SODIUM ACETATE, 200MM CALCIUM ACETA 30% PEG400, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.389 α = 90 b = 131.838 β = 90 c = 108.825 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315 MIRRORS 2011-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 100 0.078 8.9 12.3 157702 -5 28.249
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 1.8 1.83 100 0.91 2.5 8.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MDR 1.8 50 152804 4752 99.93 0.15964 0.15845 0.19922 0.2018 RANDOM 32.51
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] -0.81 0.48 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.164 r_dihedral_angle_4_deg 18.354 r_dihedral_angle_3_deg 13.336 r_scangle_it 7.983 r_scbond_it 5.43 r_dihedral_angle_1_deg 5.262 r_mcangle_it 4.194 r_mcbond_it 3.022 r_angle_refined_deg 1.315 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.164 r_dihedral_angle_4_deg 18.354 r_dihedral_angle_3_deg 13.336 r_scangle_it 7.983 r_scbond_it 5.43 r_dihedral_angle_1_deg 5.262 r_mcangle_it 4.194 r_mcbond_it 3.022 r_angle_refined_deg 1.315 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10772 Nucleic Acid Atoms Solvent Atoms 1397 Heterogen Atoms 147
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling