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EQADH-NADH-4-METHYLBENZYL ALCOHOL, p21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 10 MG/ML ENZYME DIALYZED AGAINST 50 MM AMMONIUM N-[TRIS(HYDROXYLMETHYL)METHYL]2-AMINOETHANE SULFONATE (PH 6.7 AT 25 DEG C) WITH 1 MM NAD+ AND 10 MM 4-METHY-BENZYL ALCOHOL AS THE CONCENTRATION OF 2-METHYL-2,4-PENTANEDIOL WAS RAISED TO 25 %. CRYSTAL WAS MOUNTED ON A FIBER LOOP AND FLASH VITRIFIED BY
PLUNGING IT INTO LIQUID N2.
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.22 α = 90 b = 180.22 β = 106.12 c = 86.86 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 CCD MARMOSAIC 300 mm CCD 2006-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9537 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (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 1.2 19.96 99.2 0.114 0.12 7.1 9.53 456390 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 98.2 0.596 0.643 7.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5vl0 1.2 19.96 456320 2399 99.197 0.177 0.1764 0.1879 0.2102 0.2259 23.888
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] 3.305 1.473 -3.051 -0.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.358 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 6.7 r_rigid_bond_restr 4.132 r_scangle_it 2.809 r_scangle_other 2.809 r_scbond_it 2.644 r_scbond_other 2.644 r_lrange_it 2.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.358 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 6.7 r_rigid_bond_restr 4.132 r_scangle_it 2.809 r_scangle_other 2.809 r_scbond_it 2.644 r_scbond_other 2.644 r_lrange_it 2.503 r_lrange_other 2.409 r_angle_refined_deg 2.134 r_mcangle_it 1.677 r_mcangle_other 1.677 r_mcbond_it 1.588 r_mcbond_other 1.585 r_angle_other_deg 1.58 r_nbd_refined 0.212 r_nbd_other 0.187 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.135 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.117 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11140 Nucleic Acid Atoms Solvent Atoms 1248 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing