X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 7
Temperature 298.0
Details 20% PEG 3350 and 0.2 M NaI, pH 7.0, under parafin oil, temperature 298K, Microbatch

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.35 α = 90
b = 77.27 β = 90
c = 132.44 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Oxford Danfysik toroidal focusing mirror. 2008-02-28
Diffraction Radiation
Monochromator Protocol
Monochromator: Si(111) channel cut monochromator. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 1.000 NSLS X6A

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
1.63 50 99.3 -- 0.072 -- 7.2 83995 83444 3.0 1.0 --
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)
1.63 1.69 93.5 -- 0.51 2.3 4.1 7804

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 1.63 26.57 0.0 0.0 83995 79699 4185 99.73 -- 0.144 0.143 0.169 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 1.63 1.673 5611 286 5611 0.212 0.259 -- 96.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.9
Anisotropic B[1][1] -0.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.23
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.203
r_gen_planes_other 0.001
r_mcbond_other 0.318
r_bond_refined_d 0.01
r_chiral_restr 0.08
r_nbd_refined 0.219
r_nbtor_other 0.083
r_symmetry_vdw_other 0.228
r_symmetry_hbond_refined 0.195
r_xyhbond_nbd_refined 0.163
r_scangle_it 4.418
r_symmetry_vdw_refined 0.183
r_mcbond_it 1.23
r_bond_other_d 0.001
r_angle_refined_deg 1.374
r_dihedral_angle_3_deg 10.805
r_dihedral_angle_2_deg 32.809
r_angle_other_deg 0.93
r_nbtor_refined 0.181
r_dihedral_angle_4_deg 16.732
r_mcangle_it 1.954
r_scbond_it 3.066
r_dihedral_angle_1_deg 6.607
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4753
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 682

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data collection