1Z84

X-ray structure of galt-like protein from arabidopsis thaliana at5g18200


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VKVPDB ENTRY 1VKV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.529310 MG/ML PROTEIN, 20% PEG 2000, 0.2M Sodium Chloride, 0.10M MES-Acetate, vapor diffusion, hanging drop, temperature 293K, pH 5.50
Crystal Properties
Matthews coefficientSolvent content
2.447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.037α = 90
b = 95.65β = 90
c = 110.918γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR2004-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
11.83434.48696.50.08315.2496.957501
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)
1.831.971.40.3864.5435.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1VKV1.8331.2854539290398.10.188330.1860.231RANDOM24.85
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.991
r_dihedral_angle_4_deg23.577
r_dihedral_angle_3_deg13.334
r_dihedral_angle_1_deg6.304
r_scangle_it3.653
r_scbond_it2.545
r_angle_refined_deg1.558
r_mcangle_it1.539
r_mcbond_it0.932
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.991
r_dihedral_angle_4_deg23.577
r_dihedral_angle_3_deg13.334
r_dihedral_angle_1_deg6.304
r_scangle_it3.653
r_scbond_it2.545
r_angle_refined_deg1.558
r_mcangle_it1.539
r_mcbond_it0.932
r_nbtor_refined0.307
r_nbd_refined0.207
r_symmetry_vdw_refined0.207
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.169
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4884
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms72

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement