X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 277.0
Details 2.5M NaCl, 0.1M Potassium phosphate pH6.2, 5MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.47 α = 90
b = 102.79 β = 90
c = 137.03 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Bruker DIP-6040 -- 2004-07-07
IMAGE PLATE DIP6040 -- 2004-09-23
Diffraction Radiation
Monochromator Protocol
-- MAD
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU

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
2.5 80 96.0 -- 0.071 -- 12.5 -- 19261 -- -- 59.41
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)
2.5 2.59 96.6 -- 0.311 3.5 6.7 --

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 2.5 30.0 -- -- -- 18065 932 98.39 -- 0.20302 0.20107 0.2415 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 2.5 2.565 -- 71 1272 0.281 0.33 -- 95.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.352
Anisotropic B[1][1] 2.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.2
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.25
r_symmetry_vdw_refined 0.26
r_bond_refined_d 0.028
r_gen_planes_refined 0.009
r_scbond_it 3.42
r_xyhbond_nbd_other 0.183
r_xyhbond_nbd_refined 0.166
r_scangle_it 5.633
r_dihedral_angle_2_deg 34.483
r_nbtor_refined 0.34
r_dihedral_angle_4_deg 23.6
r_dihedral_angle_3_deg 22.192
r_angle_refined_deg 2.503
r_nbd_refined 0.276
r_mcbond_it 1.141
r_mcangle_it 2.171
r_dihedral_angle_1_deg 8.983
r_chiral_restr 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3302
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 36

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
DENZO data reduction
SCALEPACK data scaling
SHARP phasing