X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.4
Temperature 298.0
Details 30% PEG 4000, 100 mM Tris, 2 mM DTT, 100 mM lithium sulfate, pH 8.4, VAPOR DIFFUSION, SITTING DROP at 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.02 α = 90
b = 106.22 β = 90
c = 114.36 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 190
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 double crystals 2001-11-23
Diffraction Radiation
Monochromator Protocol
double crystals SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.000 SSRL BL9-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.2 30 100.0 0.103 -- -- 13.8 -- 35346 -- 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.24 100.0 0.648 -- 2.2 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.2 30.0 -- 0.0 35344 35344 1858 99.92 0.221 0.22115 0.21966 0.24834 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.257 -- 125 2570 0.255 0.287 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.323
Anisotropic B[1][1] 0.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.455
r_gen_planes_refined 0.007
r_chiral_restr 0.128
r_dihedral_angle_3_deg 21.812
r_dihedral_angle_1_deg 3.881
r_angle_refined_deg 1.741
r_bond_refined_d 0.017
p_angle_d 1.741
p_angle_deg 1.741
p_bond_d 0.017
r_nbd_refined 0.322
r_xyhbond_nbd_refined 0.289
r_symmetry_vdw_refined 0.292
r_symmetry_hbond_refined 0.214
r_mcbond_it 0.845
r_mcangle_it 1.524
r_scbond_it 2.829
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4183
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 340

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection