X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 291.0
Details 45%(v/v) methanol, 50 mM HEPES pH 6.4 and 100 mM Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.67 α = 90
b = 38.82 β = 100.87
c = 56.64 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2006-12-20
Diffraction Radiation
Monochromator Protocol
Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 1.817 EMBL/DESY, HAMBURG X11

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
1.4 55.7 99.5 -- -- -- -- 22394 22394 0.0 0.0 --
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)
1.4 1.45 97.7 -- -- -- -- --

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 1.401 55.64 -- 0.0 22275 22275 1142 98.96 -- 0.1602 0.1587 0.1877 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 1.401 1.438 -- 84 1388 0.285 0.299 -- 89.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.6643
Anisotropic B[1][1] -0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.16
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 6.722
r_scbond_it 4.055
r_mcangle_it 2.434
r_mcbond_it 1.363
r_gen_planes_refined 0.011
r_chiral_restr 0.147
r_dihedral_angle_4_deg 16.153
r_dihedral_angle_3_deg 13.593
r_dihedral_angle_2_deg 40.474
r_dihedral_angle_1_deg 3.449
r_angle_refined_deg 2.405
r_bond_refined_d 0.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 910
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 169

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0072 refinement