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Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PMQ PDB ENTRY 2PMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Protein (17 mb\g/ml, 5mM Mg2+, 20mM Tris buffer (pH=7.9), 5% glycerol); Reservoir (40 % w/v pentaerythritol propoxylate (17/8 PO/OH) 0.2 M magnesium chloride 5.5 0.1 M MES-NaOH (MIDAS F8)); Cryoprotection (Reservoir), pH 6.5, sitting drop, vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.313 α = 90 b = 154.897 β = 90 c = 181.983 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 RAYONIX MX225HE MIRRORS 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.2 181.983 99.9 0.184 0.184 9.3 7.3 158072 158072 23.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.8 0.804 0.804 0.9 7.1 22827
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2PMQ 2.2 40.809 157964 157964 7926 99.88 0.1536 0.1536 0.1503 0.155 0.216 0.2152 RANDOM 29.9691
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.072 f_angle_d 1.384 f_chiral_restr 0.079 f_bond_d 0.014 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21977 Nucleic Acid Atoms Solvent Atoms 1878 Heterogen Atoms 23
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction AMoRE phasing