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GDH-105 crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1000281600
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Crystals were grown in 30% PEG4000 with 200 mM malate imidazole buffer at pH 6.0. Sitting drops were 200 nL of reservoir with 200 nL of protein at about 10 mg/mL at room temperature.
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.336 α = 90 b = 120.428 β = 101.891 c = 125.775 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.66 49 98 0.141 0.058 0.997 9.3 6.9 212485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 88.9 1.323 0.541 0.609 1.4 6.8
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 FREE R-VALUE 1.66 49 212442 10634 97.883 0.174 0.1731 0.1847 0.1965 0.2056 22.442
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] -0.843 1.475 -0.868 1.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.268 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 5.998 r_lrange_it 5.779 r_lrange_other 5.773 r_dihedral_angle_2_deg 5.495 r_scangle_it 4.58 r_scangle_other 4.58 r_scbond_it 3.013 r_scbond_other 3.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.268 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 5.998 r_lrange_it 5.779 r_lrange_other 5.773 r_dihedral_angle_2_deg 5.495 r_scangle_it 4.58 r_scangle_other 4.58 r_scbond_it 3.013 r_scbond_other 3.013 r_mcangle_other 2.909 r_mcangle_it 2.908 r_mcbond_it 2.048 r_mcbond_other 2.048 r_angle_refined_deg 1.361 r_angle_other_deg 0.46 r_symmetry_xyhbond_nbd_refined 0.311 r_nbd_other 0.309 r_symmetry_nbd_refined 0.291 r_nbd_refined 0.224 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_ncsr_local_group_27 0.072 r_ncsr_local_group_28 0.071 r_ncsr_local_group_13 0.066 r_ncsr_local_group_18 0.066 r_ncsr_local_group_7 0.064 r_ncsr_local_group_22 0.063 r_ncsr_local_group_25 0.063 r_ncsr_local_group_20 0.06 r_ncsr_local_group_3 0.058 r_ncsr_local_group_12 0.058 r_ncsr_local_group_26 0.058 r_ncsr_local_group_9 0.057 r_ncsr_local_group_21 0.057 r_ncsr_local_group_6 0.055 r_ncsr_local_group_24 0.054 r_ncsr_local_group_11 0.053 r_ncsr_local_group_10 0.051 r_ncsr_local_group_23 0.051 r_ncsr_local_group_4 0.05 r_ncsr_local_group_8 0.05 r_ncsr_local_group_5 0.049 r_ncsr_local_group_14 0.047 r_ncsr_local_group_16 0.047 r_ncsr_local_group_17 0.046 r_ncsr_local_group_2 0.045 r_ncsr_local_group_15 0.045 r_ncsr_local_group_1 0.043 r_ncsr_local_group_19 0.043 r_dihedral_angle_other_2_deg 0.023 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15672 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing