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Crystal structure of a human Jag1 fragment in complex with an anti-Jag1 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VJ2 2VJ2, 2R0L experimental model PDB 2R0L 2VJ2, 2R0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 292 100 mM CHES pH 9.5, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.258 α = 90 b = 80.978 β = 94.39 c = 155.616 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 80 PIXEL PSI PILATUS 6M 2014-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9537 SSRL BL12-2
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 2.56 71.79 96.6 0.13 6.4 3.3 41207 59.89
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 2.56 2.86 97.9 0.57 1.8 3.3
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 2VJ2, 2R0L 2.56 71.79 41207 2075 96.4 0.222 0.22 0.2294 0.259 0.2472 RANDOM 41.55
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] 3.4702 1.5005 1.0991 -4.5693
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.7 t_omega_torsion 2.65 t_angle_deg 1.06 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.7 t_omega_torsion 2.65 t_angle_deg 1.06 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8746 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 12
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHENIX phasing iMOSFLM data reduction