X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 35% PEG8K, 0.2 M ammonium sulfate, pH 6.2, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.33 α = 90
b = 131.22 β = 97.6
c = 88.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 MICROMAX CONFOCAL 2005-04-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.541 -- --

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
2.65 50 99.8 0.135 -- -- 3.7 -- 56952 -- -- --
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)
2.65 2.74 99.0 0.49 -- -- 3.5 5619

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 2.65 44.08 -- 0.0 -- 56926 2884 99.76 -- 0.2196 0.2171 0.2669 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 2.65 -- -- 206 3910 0.288 0.317 -- 98.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8044
Anisotropic B[1][1] -1.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.16
Anisotropic B[2][2] -1.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.33
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.562
r_scbond_it 0.935
r_mcangle_it 0.8
r_mcbond_it 0.431
r_symmetry_hbond_refined 0.192
r_bond_refined_d 0.009
r_angle_refined_deg 1.364
r_dihedral_angle_1_deg 5.927
r_dihedral_angle_2_deg 35.297
r_dihedral_angle_3_deg 15.56
r_dihedral_angle_4_deg 15.099
r_chiral_restr 0.091
r_gen_planes_refined 0.004
r_nbd_refined 0.194
r_nbtor_refined 0.309
r_xyhbond_nbd_refined 0.153
r_symmetry_vdw_refined 0.288
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12146
Nucleic Acid Atoms 0
Heterogen Atoms 129
Solvent Atoms 435

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0019 refinement
CNS molecular replacement
SCALEPACK data reduction