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Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EJC PDB entry 2EJC modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 290 JCSG+ Screen B3: 20% PEG 6000, 100mM Bicine pH 9.0. Protein at 22 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.32 α = 90 b = 94.32 β = 90 c = 236.93 γ = 120
Symmetry Space Group P 31 2 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 CCD MARMOSAIC 325 mm CCD 2009-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.1 50 99.8 0.059 27.31 8.9 72100 72100 -3 39.63
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) 2.1 2.15 99.9 0.525 3.9 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB entry 2EJC modified with ccp4 program chainsaw 2.1 47.95 72027 72027 3633 99.8 0.196 0.196 0.194 0.1979 0.245 0.2477 RANDOM 27.67
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] 0.66 0.33 0.66 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 5.902 r_scangle_it 3.665 r_scbond_it 2.247 r_angle_refined_deg 1.443 r_mcangle_it 1.376 r_angle_other_deg 0.879 r_mcbond_it 0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 5.902 r_scangle_it 3.665 r_scbond_it 2.247 r_angle_refined_deg 1.443 r_mcangle_it 1.376 r_angle_other_deg 0.879 r_mcbond_it 0.758 r_mcbond_other 0.174 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8647 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 99
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling