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CRYSTAL STRUCTURE of AMIDOHYDROLASE PMI1525 (TARGET EFI-500319) FROM PROTEUS MIRABILIS HI4320, A COMPLEX WITH BUTYRIC ACID AND MANGANESE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1M BIS-TRIS, PH 5.5, 200MM LITHIUM SULFATE, 25% PEG3350; CRYOPROTECTION: 50MM 4-NITRO-PHENOLBUTYRATE PLUS RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.41 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.269 α = 90 b = 101.269 β = 90 c = 65.493 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 315 MIRRORS 2013-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.65 50 99.8 0.05 0.05 34.6 9.1 46783 -5
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 1.65 1.68 100 0.66 0.66 3.1 9
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 MOLECULAR REPLACEMENT THROUGHOUT 3RHG 1.65 36.46 45276 1450 99.69 0.15627 0.15544 0.1677 0.18148 0.1923 RANDOM 27.038
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] -0.48 -0.48 -0.48 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_4_deg 12.269 r_dihedral_angle_1_deg 5.769 r_angle_refined_deg 1.567 r_angle_other_deg 0.848 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_4_deg 12.269 r_dihedral_angle_1_deg 5.769 r_angle_refined_deg 1.567 r_angle_other_deg 0.848 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 18
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling