4V00 | pdb_00004v00

Structural and functional characterization of a novel monotreme- specific protein from the milk of the platypus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.6281THE PROTEIN WAS AT 4 MG/ML IN TRIS BUFFERED SALINE; THE RESERVOIR WAS 68 MM AMMONIUM ACETATE, 25.1% W/V PEG 8K, 100 MM SODIUM CACODYLATE BUFFER AT PH 6.6; DONE AT 8C.
Crystal Properties
Matthews coefficientSolvent content
2.7354.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.152α = 80.15
b = 59.721β = 82.98
c = 63.074γ = 89.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2013-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

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
11.8246.7599.50.0915.17.472773
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)
11.821.8691.20.812.26.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.8261.6869095367699.420.167020.165910.17680.187860.1929RANDOM21.003
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]
0.110.530.390.24-0.24-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.519
r_dihedral_angle_4_deg15.162
r_dihedral_angle_3_deg13.376
r_dihedral_angle_1_deg6.307
r_scbond_it1.817
r_mcangle_it1.771
r_angle_refined_deg1.162
r_mcbond_it1.125
r_mcbond_other1.123
r_angle_other_deg0.791
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.519
r_dihedral_angle_4_deg15.162
r_dihedral_angle_3_deg13.376
r_dihedral_angle_1_deg6.307
r_scbond_it1.817
r_mcangle_it1.771
r_angle_refined_deg1.162
r_mcbond_it1.125
r_mcbond_other1.123
r_angle_other_deg0.791
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms5425
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
PHASERphasing
REFMACrefinement