2VDX

Crystal Structure of the reactive loop Cleaved Corticosteroid Binding Globulin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QMNPDB ENTRY 1QMN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.410-20% PEG3350, 0.2M NACL, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
1.8948

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.941α = 81.94
b = 39.74β = 84.06
c = 112.113γ = 65.39
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray297CCDMARRESEARCH2007-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8455.4960.078.72.2517062
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.9494.10.351.52.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QMN1.8455.47490612643960.1940.1920.241RANDOM27.87
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]
1.28-0.341.060.85-0.22-2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_4_deg17.817
r_dihedral_angle_3_deg15.993
r_dihedral_angle_1_deg6.583
r_scangle_it2.528
r_scbond_it1.66
r_angle_refined_deg1.272
r_mcangle_it1.033
r_mcbond_it0.562
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_4_deg17.817
r_dihedral_angle_3_deg15.993
r_dihedral_angle_1_deg6.583
r_scangle_it2.528
r_scbond_it1.66
r_angle_refined_deg1.272
r_mcangle_it1.033
r_mcbond_it0.562
r_nbtor_refined0.301
r_nbd_refined0.199
r_symmetry_vdw_refined0.155
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.123
r_metal_ion_refined0.118
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_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 AtomsNumber
Protein Atoms5703
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing