6AY7

Cartilage homing cysteine-dense-peptides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ATM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22980.2M Na chloride, 0.1M Phosphate-citrate pH 4.2, 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
1.8332.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.838α = 90
b = 47.125β = 90
c = 48.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442017-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.775080.90.0560.02532.45.45643
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.89.90.110.1060.9958.41.6

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 REPLACEMENTTHROUGHOUT6ATM1.7733.81531030485.440.142680.139690.19262RANDOM16.713
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]
0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.661
r_dihedral_angle_4_deg18.848
r_dihedral_angle_3_deg14.597
r_long_range_B_other9.642
r_long_range_B_refined9.616
r_scangle_other7.129
r_dihedral_angle_1_deg6.124
r_scbond_it4.831
r_scbond_other4.619
r_mcangle_other2.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.661
r_dihedral_angle_4_deg18.848
r_dihedral_angle_3_deg14.597
r_long_range_B_other9.642
r_long_range_B_refined9.616
r_scangle_other7.129
r_dihedral_angle_1_deg6.124
r_scbond_it4.831
r_scbond_other4.619
r_mcangle_other2.882
r_mcangle_it2.878
r_mcbond_it1.961
r_mcbond_other1.94
r_angle_refined_deg1.528
r_angle_other_deg0.871
r_chiral_restr0.407
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms592
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms31

Software

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