1JIQ

Crystal Structure of Human Autocrine Motility Factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DQRPDB ENTRY 1DQR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.77α = 90
b = 107.4β = 90
c = 270.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-18BPhoton FactoryBL-18B

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
11.94098.70.1084.67.4183404
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)
1.9292.10.3052.44.4

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 1DQR1.936174100919598.690.1690.167470.19791RANDOM15.102
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]
0.360.68-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.32
r_dihedral_angle_1_deg4.131
r_scangle_it2.866
r_scbond_it1.747
r_angle_refined_deg1.321
r_mcangle_it1.089
r_angle_other_deg0.759
r_mcbond_it0.59
r_symmetry_vdw_refined0.284
r_nbd_refined0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.32
r_dihedral_angle_1_deg4.131
r_scangle_it2.866
r_scbond_it1.747
r_angle_refined_deg1.321
r_mcangle_it1.089
r_angle_other_deg0.759
r_mcbond_it0.59
r_symmetry_vdw_refined0.284
r_nbd_refined0.228
r_symmetry_hbond_refined0.209
r_nbd_other0.196
r_symmetry_vdw_other0.174
r_xyhbond_nbd_other0.151
r_xyhbond_nbd_refined0.137
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbtor_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17780
Nucleic Acid Atoms
Solvent Atoms1475
Heterogen Atoms

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling