X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 30% PEG 4000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.66 α = 90
b = 95.66 β = 90
c = 201.46 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 197
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2004-11-14
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2

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
2.7 30 95.0 0.075 0.054 -- -- 30133 28495 2.0 2.0 --

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 2.75 20.0 2.0 2.0 -- 23062 1223 85.49 -- 0.24741 0.24486 0.29548 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 2.75 2.82 -- 74 1312 0.282 0.346 -- 68.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.027
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.18
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.53
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.37
r_scbond_it 0.808
r_mcangle_it 0.761
r_mcbond_it 0.422
r_symmetry_hbond_refined 0.08
r_bond_refined_d 0.009
r_angle_refined_deg 1.15
r_dihedral_angle_1_deg 4.968
r_dihedral_angle_2_deg 34.805
r_dihedral_angle_3_deg 17.703
r_dihedral_angle_4_deg 16.264
r_chiral_restr 0.078
r_gen_planes_refined 0.003
r_nbd_refined 0.203
r_nbtor_refined 0.303
r_xyhbond_nbd_refined 0.158
r_symmetry_vdw_refined 0.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7428
Nucleic Acid Atoms 638
Heterogen Atoms 20
Solvent Atoms 114

Software

Computing
Computing Package Purpose
ProDC Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement