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Crystal Structure of Yeast NADH Kinase complexed with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AN1 PDB ENTRY 2AN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 15% 2-methyl-2,4-pentanediol, 5% PEG 4000, 100mM imidazole-HCl, 5mM NADH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.685 α = 90 b = 132.782 β = 90 c = 59.636 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 210 2009-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 1.93 50 99.5 0.064 16.8 8 59896
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) 1.93 2 99 0.399 5.92 7 5835
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 2AN1 2 50 50821 2702 99.51 0.19974 0.19742 0.1973 0.24383 0.2451 RANDOM 30.887
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] -0.66 0.97 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.027 r_dihedral_angle_4_deg 15.756 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 5.905 r_scangle_it 2.409 r_scbond_it 1.419 r_mcangle_it 1.208 r_angle_refined_deg 1.187 r_mcbond_it 0.659 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.027 r_dihedral_angle_4_deg 15.756 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 5.905 r_scangle_it 2.409 r_scbond_it 1.419 r_mcangle_it 1.208 r_angle_refined_deg 1.187 r_mcbond_it 0.659 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 5462 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling