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Rabbit muscle glycogen phosphorylase b in complex with N-(pyridyl-2- carbonyl)-N-beta-D-glucopyranosyl urea determined at 2.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QNB PDB ENTRY 2QNB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.414 α = 90 b = 128.414 β = 90 c = 116.523 γ = 90
Symmetry Space Group P 43 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 298 CCD MARRESEARCH SX-165 2007-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.05 30 99 0.05 21.2 5.3 61537
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 2.05 2.09 99.1 0.42 4.1 5.3
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 PDB ENTRY 2QNB 2.05 24.08 58355 3113 99.93 0.1867 0.18514 0.1839 0.21588 0.2153 RANDOM 32.039
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] 0.06 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.665 r_dihedral_angle_4_deg 18.717 r_dihedral_angle_3_deg 14.232 r_dihedral_angle_1_deg 5.203 r_scangle_it 2.254 r_scbond_it 1.284 r_angle_refined_deg 1.004 r_mcangle_it 0.949 r_mcbond_it 0.487 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.665 r_dihedral_angle_4_deg 18.717 r_dihedral_angle_3_deg 14.232 r_dihedral_angle_1_deg 5.203 r_scangle_it 2.254 r_scbond_it 1.284 r_angle_refined_deg 1.004 r_mcangle_it 0.949 r_mcbond_it 0.487 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_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 6569 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing