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Structure of Octopine-dehydrogenase in complex with NADH and Agmatine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C7C PDB ENTRY 3C7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM sodium citrate, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.2 α = 90 b = 96.2 β = 90 c = 117.4 γ = 90
Symmetry Space Group P 41 21 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 CCD MARMOSAIC 225 mm CCD 2008-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8 ESRF ID23-2
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 2.8 74.33 90 0.103 4.5 4.5 11968 11368 45
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 2.8 2.9 92.5 0.363 4.5 4.5
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 3C7C 2.8 29.45 11368 599 100 0.20505 0.2023 0.201 0.25698 0.2526 RANDOM 28.062
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] 0.34 0.34 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.362 r_dihedral_angle_4_deg 17.797 r_dihedral_angle_3_deg 15.948 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.074 r_scangle_it 0.871 r_scbond_it 0.509 r_mcangle_it 0.418 r_nbtor_refined 0.301 r_mcbond_it 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.362 r_dihedral_angle_4_deg 17.797 r_dihedral_angle_3_deg 15.948 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.074 r_scangle_it 0.871 r_scbond_it 0.509 r_mcangle_it 0.418 r_nbtor_refined 0.301 r_mcbond_it 0.233 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3086 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling