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Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with phosphate ion at 1.71 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.153 α = 90 b = 133.153 β = 90 c = 38.397 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH MIRROR 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.71 66.6 100 0.069 13.1 27430 27430
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.77 100 0.47 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4G2X 1.71 66.58 26055 1377 99.97 0.21438 0.21221 0.25646 0.2872 RANDOM 29.078
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] -0.75 -0.75 -0.75 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_4_deg 14.085 r_dihedral_angle_1_deg 5.92 r_angle_other_deg 3.811 r_scbond_it 3.037 r_angle_refined_deg 2.143 r_mcangle_it 2.128 r_mcbond_it 1.495 r_mcbond_other 1.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_4_deg 14.085 r_dihedral_angle_1_deg 5.92 r_angle_other_deg 3.811 r_scbond_it 3.037 r_angle_refined_deg 2.143 r_mcangle_it 2.128 r_mcbond_it 1.495 r_mcbond_other 1.495 r_chiral_restr 0.161 r_bond_refined_d 0.028 r_gen_planes_other 0.015 r_gen_planes_refined 0.01 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling