2VDB

Structure of human serum albumin with S-naproxen and the GA module


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E7EPDB ENTRIES 1E7E AND 1TF0
experimental modelPDB 1TF0PDB ENTRIES 1E7E AND 1TF0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
126-32% PEG 3350, 50 MM POTASSIUM PHOSPHATE, 0.1 M AMMONIUM PHOSPHATE/POTASSIUM PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
2.5251

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.507α = 90
b = 49.462β = 93
c = 79.933γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2006-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.580.32990.1412.226.33248473.758.71
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)
12.52.5298.30.361.953.69

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 ENTRIES 1E7E AND 1TF02.5294.9224846127396.70.2360.2340.28RANDOM57.55
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]
-1.8910.1982.076-0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.133
r_dihedral_angle_4_deg19.905
r_dihedral_angle_3_deg17.692
r_dihedral_angle_1_deg6.058
r_mcangle_it1.385
r_angle_refined_deg1.371
r_scangle_it1.277
r_scbond_it0.865
r_mcbond_it0.863
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.133
r_dihedral_angle_4_deg19.905
r_dihedral_angle_3_deg17.692
r_dihedral_angle_1_deg6.058
r_mcangle_it1.385
r_angle_refined_deg1.371
r_scangle_it1.277
r_scbond_it0.865
r_mcbond_it0.863
r_nbtor_refined0.32
r_nbd_refined0.265
r_symmetry_vdw_refined0.255
r_xyhbond_nbd_refined0.199
r_chiral_restr0.094
r_symmetry_hbond_refined0.033
r_bond_refined_d0.017
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4783
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
MOLREPphasing