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Structure of IDP00107, a potential N-acetyl-gamma-glutamylphosphate reductase from Shigella flexneri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G17 protein atoms from 2G17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 2.2 M D,L-Malic Acid and 0.1 M Bis-Tris Propane. Cryoprotected with N-paratone oil, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.299 α = 90 b = 117.299 β = 90 c = 115.472 γ = 120
Symmetry Space Group P 62 2 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 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2008-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 50 99.7 0.108 31.4 16.8 32274 32186
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 2.07 99.3 0.454 10.1 16
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 (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 protein atoms from 2G17 2 24.81 32141 30510 1631 99.8 0.16838 0.16593 0.1682 0.21623 0.2187 RANDOM 22.184
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 r_dihedral_angle_2_deg 34.685 r_dihedral_angle_4_deg 17.862 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.803 r_scangle_it 3.618 r_scbond_it 2.344 r_angle_refined_deg 1.549 r_mcangle_it 1.517 r_mcbond_it 0.865 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.685 r_dihedral_angle_4_deg 17.862 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.803 r_scangle_it 3.618 r_scbond_it 2.344 r_angle_refined_deg 1.549 r_mcangle_it 1.517 r_mcbond_it 0.865 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.111 r_metal_ion_refined 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_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 2551 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing