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Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with (3-(Trimethylammonio)propyl)phosphinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O2G PDB ENTRY 3O2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 20 % PEG 3350, 1.5 % 1.6-DIAMINOHEXANE, 200 MM AMMONIUM CITRATE PH 7.0, 10 MM ZNSO4, 8 MM N-OXALYLGLYCINE, 4 MM INHIBITOR, PROTEIN 6.5 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-7 DAYS
Crystal Properties Matthews coefficient Solvent content 2.5 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.72 α = 90 b = 107.72 β = 90 c = 204.71 γ = 120
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 MARRESEARCH MIRRORS 2011-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 2.18 37.55 97.9 0.13 6.2 2.5 23613 21.614
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) 1 2.18 2.3 99.5 0.45 2.2 2.5
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 PDB ENTRY 3O2G 2.18 42.44 22547 1216 98.57 0.148 0.14554 0.1551 0.19365 0.2037 RANDOM 21.266
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] 0.1 0.1 0.1 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 12.698 r_dihedral_angle_1_deg 6.381 r_angle_refined_deg 1.344 r_angle_other_deg 0.721 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 12.698 r_dihedral_angle_1_deg 6.381 r_angle_refined_deg 1.344 r_angle_other_deg 0.721 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 3116 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling