X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.9
Temperature 293.0
Details 0.2 M Ca acetate, 0.1 M Na cacodilate, 9% PEG 8K, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.77 α = 90
b = 92.04 β = 90
c = 96.21 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRROR 2008-11-21
Diffraction Radiation
Monochromator Protocol
SI-111 CHANNEL single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9786 APS 19-ID

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 50 93.7 0.091 0.091 -- 6.5 34443 34443 0.0 -3.0 --
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)
2.0 2.03 88.0 0.513 0.513 2.8 5.9 1520

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
SAD 2.0 50.0 0.0 0.0 34327 34327 1714 93.86 0.187 0.187 0.185 0.239 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 2.0 2.05 -- 123 2221 0.242 0.282 -- 87.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.14
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.55
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.135
r_scbond_it 2.698
r_mcangle_it 1.617
r_mcbond_other 0.296
r_mcbond_it 0.959
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.104
r_dihedral_angle_4_deg 15.007
r_dihedral_angle_3_deg 13.975
r_dihedral_angle_2_deg 41.118
r_dihedral_angle_1_deg 6.303
r_angle_other_deg 0.999
r_angle_refined_deg 1.75
r_bond_other_d 0.006
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3771
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 408

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
HKL-3000, MLPHARE, DM, SHELXD, RESOLVE, ARP/WARP Structure Solution
REFMAC 5.5.0072, COOT Structure Refinement
Software
Software Name Purpose
COOT refinement
REFMAC version: 5.5.0072 refinement
ARP/WARP model building
RESOLVE model building
SHELXD model building
DM model building
MLPHARE model building
HKL-3000 model building
HKL-3000 data collection