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_scbond_it 0.808
r_symmetry_hbond_refined 0.08
r_dihedral_angle_3_deg 17.703
r_gen_planes_refined 0.003
r_nbd_refined 0.203
r_symmetry_vdw_refined 0.167
r_mcangle_it 0.761
r_dihedral_angle_1_deg 4.968
r_scangle_it 1.37
r_nbtor_refined 0.303
r_mcbond_it 0.422
r_angle_refined_deg 1.15
r_dihedral_angle_4_deg 16.264
r_dihedral_angle_2_deg 34.805
r_xyhbond_nbd_refined 0.158
r_bond_refined_d 0.009
r_chiral_restr 0.078
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

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
ProDC data collection
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing