X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details VAPOUR DIFFUSION HANGING DROP PROTEIN SOLUTION: 10 MG/ML IN 50 MM TRIS-HCL PH 7.0, 1 MM DTT, 20 MICROMOLAR PMSF RESERVOIR: 0.1 M SODIUM ACETATE,0.2 M AMMONIUM SULPHATE, 28% (V/V) PEG 4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.95 α = 90
b = 130.41 β = 114.16
c = 81.32 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC MIRRORS 2001-09-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.97900,0.97937,0.88560 ESRF BM14

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 30 99.7 0.043 -- -- 3.4 -- 95532 -- -- --
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 97.0 0.157 -- 7.1 3.4 --

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 2.0 25.0 -- -- -- 95532 5022 99.6 -- 0.149 0.147 0.19 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 -- 319 6225 0.163 0.209 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.57
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.86
Anisotropic B[2][2] -0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.38
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.881
r_scbond_it 2.464
r_mcangle_it 1.536
r_mcbond_it 0.858
r_nbd_refined 0.227
r_gen_planes_other 0.005
r_gen_planes_refined 0.007
r_chiral_restr 0.108
r_dihedral_angle_1_deg 6.011
r_angle_other_deg 1.082
r_angle_refined_deg 1.63
r_bond_other_d 0.002
r_bond_refined_d 0.017
r_nbd_other 0.255
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.171
r_metal_ion_refined 0.064
r_symmetry_vdw_refined 0.256
r_symmetry_vdw_other 0.296
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11443
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 1009

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
SOLVE model building