X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details PEG 2000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.47 α = 90
b = 40.66 β = 90
c = 76.15 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-07-14
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 1.0092, 1.0011, 1.0076 NSLS X9B

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
1.05 36 87.9 -- 0.035 -- 8.5 45991 43635 -- -3.0 8.0
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)
1.05 1.09 44.3 -- 0.488 -- 3.9 2277

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 1.05 35.81 -- 0.0 -- 43635 2306 87.96 -- 0.15647 0.15595 0.16615 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 1.05 1.077 -- 79 1512 0.292 0.29 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.08
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.709
r_symmetry_vdw_other 0.143
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_symmetry_vdw_refined 0.339
r_dihedral_angle_3_deg 19.459
r_bond_refined_d 0.007
r_scangle_it 3.297
r_xyhbond_nbd_refined 0.227
r_symmetry_hbond_refined 0.286
r_scbond_it 2.225
r_mcbond_it 1.029
r_mcangle_it 1.668
r_nbd_refined 0.224
r_bond_other_d 0.001
r_angle_other_deg 0.686
r_nbd_other 0.208
r_angle_refined_deg 1.478
r_chiral_restr 0.085
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 827
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 178

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CNS refinement
REFMAC refinement version: 5.0
HKL-2000 data reduction
CNS phasing