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Crystal structure of the recombinant variable domain 6JAL2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CD0 PDB ENTRY 2CD0
Crystallization Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.267 α = 90 b = 71.267 β = 90 c = 95.452 γ = 90
Symmetry Space Group P 41 2 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 CCD 2005-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 2.35 50.19 87.9 0.05 15.5 3 9289 48.46
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 2.35 2.48 92.4 0.39 2.8 2.9
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 2CD0 2.35 22.63 8802 441 86 0.212 0.209 0.2092 0.242 0.254 RANDOM 41.24
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] 0.29 0.29 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.01 r_dihedral_angle_3_deg 22.236 r_dihedral_angle_4_deg 19.335 r_dihedral_angle_1_deg 8.379 r_angle_refined_deg 3.124 r_scangle_it 2.5 r_scbond_it 1.964 r_mcangle_it 1.173 r_mcbond_it 0.859 r_symmetry_vdw_refined 0.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.01 r_dihedral_angle_3_deg 22.236 r_dihedral_angle_4_deg 19.335 r_dihedral_angle_1_deg 8.379 r_angle_refined_deg 3.124 r_scangle_it 2.5 r_scbond_it 1.964 r_mcangle_it 1.173 r_mcbond_it 0.859 r_symmetry_vdw_refined 0.388 r_nbtor_refined 0.339 r_nbd_refined 0.303 r_xyhbond_nbd_refined 0.23 r_chiral_restr 0.207 r_symmetry_hbond_refined 0.15 r_bond_refined_d 0.032 r_gen_planes_refined 0.013 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing