X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 27% PEG 400, 0.1 M HEPES pH 7.5, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.86 α = 90
b = 114.86 β = 90
c = 126.08 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-06-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.97946 SSRL BL9-1

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
1.93 50 99.9 0.076 -- -- 28.5 -- 63820 -- -- --
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)
1.93 2.0 98.8 0.321 -- -- 25.2 6209

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 1.93 42.45 -- 0.0 -- 63734 3234 99.89 -- 0.159 0.158 0.18 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 1.93 1.981 -- 236 4371 0.196 0.243 -- 98.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.338
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.17
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 10.423
r_symmetry_hbond_refined 0.204
r_scangle_it 7.18
r_dihedral_angle_1_deg 4.614
r_chiral_restr 0.06
r_scbond_it 5.023
r_dihedral_angle_4_deg 13.513
r_xyhbond_nbd_refined 0.174
r_nbd_refined 0.188
r_angle_refined_deg 0.865
r_symmetry_vdw_refined 0.173
r_bond_refined_d 0.005
r_gen_planes_refined 0.002
r_mcbond_it 4.078
r_mcangle_it 4.381
r_dihedral_angle_2_deg 30.796
r_nbtor_refined 0.319
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3516
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 775

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection