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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Ambient temperature, Serial crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 293 32% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.5 α = 90 b = 129.6 β = 90 c = 151.9 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER R 4M 2025-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 HARE chip fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 HARE chip HARE chip HARE chip Mother liquor
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.93 98.787 100 0.9146 0.2854 2.99 73.2 102629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.01 100 0.3768 1.0805 1.02 50.3
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 1.93 98.787 102533 5168 99.996 0.187 0.1849 0.1897 0.2224 0.2255 27.871
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] 0.157 -0.778 0.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 7.237 r_lrange_it 5.42 r_lrange_other 5.409 r_scangle_other 4.051 r_scangle_it 4.043 r_mcangle_it 3.042 r_mcangle_other 3.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 7.237 r_lrange_it 5.42 r_lrange_other 5.409 r_scangle_other 4.051 r_scangle_it 4.043 r_mcangle_it 3.042 r_mcangle_other 3.042 r_scbond_other 2.518 r_scbond_it 2.513 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.504 r_angle_other_deg 1.258 r_nbd_other 0.22 r_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.124 r_symmetry_nbd_refined 0.086 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.027 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 9217 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing