X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 289.0
Details 0.2M sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.93 α = 90
b = 84.13 β = 109.06
c = 58.22 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 -- 2005-04-07
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM

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
2.25 55.05 -- 0.118 -- -- -- 24225 24141 -- -- --
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)
2.25 2.33 59.7 0.564 -- 2.0 2.9 --

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 2.25 27.01 -- -- -- 22883 1233 99.57 -- 0.18756 0.18519 0.23141 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 2.252 2.31 -- 73 1617 0.265 0.362 -- 95.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.764
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 5.567
r_mcangle_it 4.221
r_dihedral_angle_1_deg 3.828
r_xyhbond_nbd_refined 0.239
r_dihedral_angle_2_deg 39.092
r_dihedral_angle_3_deg 14.667
r_symmetry_vdw_refined 0.202
r_nbd_refined 0.23
r_dihedral_angle_4_deg 20.873
r_gen_planes_refined 0.005
r_chiral_restr 0.178
r_angle_refined_deg 1.171
r_scangle_it 6.473
r_symmetry_hbond_refined 0.179
r_mcbond_it 3.57
r_bond_refined_d 0.011
r_nbtor_refined 0.319
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4043
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 144

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
SCALEPACK data scaling
XTALVIEW refinement