X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details MES buffer, Magnesium cloride, sodium cloride, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.63 α = 90
b = 82.63 β = 90
c = 49.15 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2002-05-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.85 25 99.8 0.045 -- -- 9.3 -- 3942 -- -- --
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)
2.85 2.95 99.8 0.45 -- -- -- --

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 2.9 20.0 -- -- -- 3394 349 99.84 -- 0.20847 0.20373 0.25507 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 2.9 2.974 -- 22 234 0.3 0.359 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.528
Anisotropic B[1][1] 0.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.02
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.11
r_nbd_other 0.227
r_nbd_refined 0.179
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.412
r_angle_other_deg 1.71
r_angle_refined_deg 1.746
r_bond_other_d 0.002
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.178
r_symmetry_vdw_refined 0.123
r_symmetry_vdw_other 0.225
r_symmetry_hbond_refined 0.149
r_scbond_it 0.853
r_scangle_it 1.372
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 842
Heterogen Atoms 43
Solvent Atoms 6

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.1.13 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.13 refinement