X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 10.5
Temperature 292.0
Details 30% PEG40, pH10.5, Microbatch under oil, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.65 α = 90
b = 53.71 β = 105.59
c = 79.33 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
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-01-01
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.15 50 94.2 0.154 0.143 -- 3.4 -- 15983 -- -- 39.86
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 83.9 0.327 0.276 2.3 2.5 1405

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 2.48 43.94 0.0 0.0 16503 15160 814 91.86 -- 0.24403 0.24233 0.27566 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 2.48 2.544 -- 45 619 0.299 0.366 -- 52.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.864
Anisotropic B[1][1] -1.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.75
Anisotropic B[2][2] -4.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.47
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.028
r_angle_refined_deg 2.511
r_gen_planes_refined 0.01
r_symmetry_hbond_refined 0.175
r_dihedral_angle_4_deg 25.248
r_scbond_it 3.548
r_dihedral_angle_3_deg 22.061
r_metal_ion_refined 0.099
r_mcbond_it 1.51
r_scangle_it 5.236
r_dihedral_angle_1_deg 9.271
r_nbtor_refined 0.325
r_mcangle_it 2.089
r_symmetry_vdw_refined 0.359
r_chiral_restr 0.177
r_xyhbond_nbd_refined 0.219
r_dihedral_angle_2_deg 36.565
r_nbd_refined 0.282
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3226
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 15

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASES phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
SCALEPACK data scaling