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Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from Bacillus licheniformis (Target NYSGRC-000337)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QAN PDB ENTRY 3QAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 0.1M SODIUM ACETATE, PH 4.6, 200MM CADMIUM CHLORIDE, 30% PEG400, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.267 α = 90 b = 116.114 β = 90.15 c = 181.768 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 ADSC QUANTUM 315 MIRRORS 2010-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 50 87.7 0.15 4.9 2.9 217382 -5 35.083
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.3 88.7 1 2.7
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 MR THROUGHOUT PDB ENTRY 3QAN 2.2 20 182882 5701 86.89 0.22433 0.22225 0.2239 0.29218 0.2942 RANDOM 45.7
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] 5.82 -0.2 -4.04 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_3_deg 18.844 r_dihedral_angle_4_deg 17.536 r_scangle_it 10.685 r_scbond_it 7.561 r_dihedral_angle_1_deg 5.784 r_mcangle_it 4.625 r_mcbond_it 3.039 r_angle_refined_deg 1.196 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_3_deg 18.844 r_dihedral_angle_4_deg 17.536 r_scangle_it 10.685 r_scbond_it 7.561 r_dihedral_angle_1_deg 5.784 r_mcangle_it 4.625 r_mcbond_it 3.039 r_angle_refined_deg 1.196 r_chiral_restr 0.086 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 31754 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 79
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling