3NK4

Crystal structure of full-length sperm receptor ZP3 at 2.0 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D4GPDB ENTRY 3D4G: PDB ENTRY 3D4G: RESIDUES 372-449 + 459-473

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP527725 MG/ML PROTEIN IN 0.1 M SODIUM CITRATE, 0.01 M TRIS-HCL, 5% PEG6000, 0.05 M SODIUM CHLORIDE, SAMPLE TO RESERVOIR RATIO IN DROP: 1:1 (DROP), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.2771.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.7α = 90
b = 97.7β = 90
c = 256.419γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9757ESRFID23-1

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
1238.999.90.09212.613.384686
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.11100213.9

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3D4G: PDB ENTRY 3D4G: RESIDUES 372-449 + 459-473236.3448457384487420999.760.20920.20830.2258RANDOM
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]
10.303110.3031-20.6061
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.388
f_angle_d1.224
f_chiral_restr0.079
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4469
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms40

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling