☰ Navigation Tabs
Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 n complex with Paranitrophenyl butyrate (PNPB)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.1M Sodium Malonate pH 7.4
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.14 60.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.313 α = 90 b = 244.89 β = 90 c = 192.097 γ = 90
Symmetry Space Group C 2 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 PIXEL RIGAKU HyPix-6000HE 2025-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.8 24.292 99.65 0.968 9.2 9.8 101792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.831
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.8 24.292 101747 5006 99.697 0.273 0.2723 0.2601 0.2937 0.2805 31.073
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] -4.575 -0.4 4.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.414 r_dihedral_angle_6_deg 14.318 r_dihedral_angle_2_deg 9.16 r_dihedral_angle_1_deg 5.776 r_angle_refined_deg 1.383 r_lrange_it 1.328 r_lrange_other 1.328 r_mcangle_it 1.034 r_mcangle_other 1.034 r_scangle_it 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.414 r_dihedral_angle_6_deg 14.318 r_dihedral_angle_2_deg 9.16 r_dihedral_angle_1_deg 5.776 r_angle_refined_deg 1.383 r_lrange_it 1.328 r_lrange_other 1.328 r_mcangle_it 1.034 r_mcangle_other 1.034 r_scangle_it 0.993 r_scangle_other 0.993 r_mcbond_it 0.686 r_mcbond_other 0.685 r_scbond_it 0.655 r_scbond_other 0.655 r_angle_other_deg 0.456 r_nbd_other 0.247 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.218 r_symmetry_nbd_other 0.208 r_symmetry_nbd_refined 0.206 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_2 0.097 r_ncsr_local_group_20 0.092 r_ncsr_local_group_10 0.09 r_ncsr_local_group_36 0.089 r_ncsr_local_group_6 0.088 r_ncsr_local_group_40 0.088 r_ncsr_local_group_23 0.087 r_ncsr_local_group_1 0.086 r_ncsr_local_group_5 0.086 r_ncsr_local_group_22 0.086 r_ncsr_local_group_3 0.085 r_ncsr_local_group_7 0.085 r_ncsr_local_group_8 0.085 r_ncsr_local_group_14 0.085 r_ncsr_local_group_18 0.085 r_ncsr_local_group_31 0.084 r_ncsr_local_group_39 0.084 r_ncsr_local_group_41 0.084 r_ncsr_local_group_19 0.082 r_ncsr_local_group_26 0.082 r_ncsr_local_group_33 0.082 r_ncsr_local_group_37 0.082 r_ncsr_local_group_38 0.082 r_ncsr_local_group_15 0.081 r_ncsr_local_group_32 0.081 r_ncsr_local_group_44 0.081 r_ncsr_local_group_4 0.08 r_ncsr_local_group_9 0.08 r_ncsr_local_group_16 0.08 r_ncsr_local_group_29 0.08 r_ncsr_local_group_13 0.079 r_ncsr_local_group_17 0.079 r_ncsr_local_group_21 0.079 r_ncsr_local_group_25 0.079 r_ncsr_local_group_42 0.079 r_ncsr_local_group_28 0.078 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_11 0.077 r_ncsr_local_group_24 0.077 r_ncsr_local_group_27 0.077 r_ncsr_local_group_34 0.077 r_ncsr_local_group_45 0.077 r_ncsr_local_group_12 0.076 r_ncsr_local_group_30 0.076 r_ncsr_local_group_35 0.073 r_ncsr_local_group_43 0.07 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22175 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing