X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details spermine, potassium chloride, MPD, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.01 α = 90
b = 35.01 β = 90
c = 22.26 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-08-20
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.8985 APS 14-BM-D

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
1.1 16.55 95.3 -- 0.037 -- 20.0 -- 5690 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)
1.1 1.14 71.9 -- 0.088 -- -- 770

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
MAD 1.1 16.55 -- 2.0 -- 5382 308 94.82 -- 0.12733 0.12678 0.13607 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 1.1 1.16 -- 34 589 0.08 0.11 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 6.497
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.53
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.673
r_nbtor_other 0.096
r_nbd_other 0.196
r_nbd_refined 0.412
r_gen_planes_refined 0.032
r_chiral_restr 0.123
r_angle_other_deg 2.098
r_angle_refined_deg 1.607
r_bond_other_d 0.003
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.121
r_symmetry_vdw_refined 0.752
r_symmetry_vdw_other 0.346
r_symmetry_hbond_refined 0.099
r_scbond_it 1.539
r_scangle_it 2.065
r_rigid_bond_restr 0.855
r_sphericity_free 8.627
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 108
Heterogen Atoms 3
Solvent Atoms 30

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement