4XX8

Crystal structure of Pro1 deletion mutant of human macrophage migration inhibitory factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52912 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.096α = 90
b = 68.155β = 90
c = 86.902γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.775099.90.04220.713.740049
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)
11.771.899.70.28612.5

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 REPLACEMENTTHROUGHOUT3DJH1.7748.1738016196999.80.1650.1640.188RANDOM18.52
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.873
r_dihedral_angle_4_deg20.699
r_dihedral_angle_3_deg12.26
r_dihedral_angle_1_deg5.484
r_angle_refined_deg2.137
r_mcangle_it2.134
r_angle_other_deg2.122
r_mcbond_it1.605
r_mcbond_other1.603
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.873
r_dihedral_angle_4_deg20.699
r_dihedral_angle_3_deg12.26
r_dihedral_angle_1_deg5.484
r_angle_refined_deg2.137
r_mcangle_it2.134
r_angle_other_deg2.122
r_mcbond_it1.605
r_mcbond_other1.603
r_chiral_restr0.127
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.008
r_gen_planes_other0.006
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2519
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing