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Crystal structure of had family enzyme bt-2542 (target efi-501088) from Bacteroides thetaiotaomicron, asp12ala mutant, complex with magnesium and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 294 0.2M MAGNESIUM FORMATE, PH 5.9, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.156 α = 90 b = 78.634 β = 90 c = 117.292 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 ADSC QUANTUM 315 MIRRORS 2012-02-22 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 2.4 70 99.1 0.087 8.7 6.9 20508 -5 62.951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.2 1.7 6.2
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 MR THROUGHOUT 4DCC 2.4 50 19578 653 98.66 0.22456 0.22233 0.2227 0.2963 0.2881 RANDOM 65.623
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] 6.15 -1.62 -4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.083 r_dihedral_angle_3_deg 15.62 r_dihedral_angle_4_deg 13.612 r_scangle_it 10.101 r_scbond_it 7.326 r_dihedral_angle_1_deg 5.273 r_mcangle_it 4.495 r_mcbond_it 2.778 r_angle_refined_deg 0.95 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.083 r_dihedral_angle_3_deg 15.62 r_dihedral_angle_4_deg 13.612 r_scangle_it 10.101 r_scbond_it 7.326 r_dihedral_angle_1_deg 5.273 r_mcangle_it 4.495 r_mcbond_it 2.778 r_angle_refined_deg 0.95 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 3265 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 29
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling