X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 1.0000M LiCl, 20.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.56 α = 82.51
b = 68.39 β = 79.52
c = 98.11 γ = 75.68
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-10
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97936,0.97917 SSRL BL9-2

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
2.1 29.88 97.6 0.069 0.069 -- 2.0 -- 92103 -- -- 25.239
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)
2.1 2.15 96.7 0.35 0.35 2.1 2.0 6769

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 2.1 29.881 -- 0.0 -- 92101 4610 97.57 -- 0.175 0.173 0.222 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 2.1 2.155 -- 348 6421 0.22 0.276 -- 96.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.74
Anisotropic B[1][1] -1.47
Anisotropic B[1][2] 0.48
Anisotropic B[1][3] 0.22
Anisotropic B[2][2] -1.69
Anisotropic B[2][3] -1.15
Anisotropic B[3][3] 3.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.922
r_scbond_it 3.038
r_mcangle_it 1.602
r_mcbond_other 0.163
r_mcbond_it 0.982
r_symmetry_hbond_refined 0.161
r_symmetry_vdw_other 0.146
r_symmetry_vdw_refined 0.112
r_xyhbond_nbd_refined 0.104
r_nbtor_other 0.072
r_nbtor_refined 0.156
r_nbd_other 0.137
r_bond_refined_d 0.015
r_bond_other_d 0.003
r_angle_refined_deg 1.618
r_angle_other_deg 1.312
r_dihedral_angle_1_deg 3.871
r_dihedral_angle_2_deg 31.234
r_dihedral_angle_3_deg 11.051
r_dihedral_angle_4_deg 13.839
r_chiral_restr 0.095
r_gen_planes_refined 0.005
r_gen_planes_other 0.002
r_nbd_refined 0.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12432
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 772

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELX/SHARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
SCALA version: 3.2.5 data processing
REFMAC5 version: 5.2.0019 refinement
SHELX phasing
phenix refinement
MOLPROBITY version: 3beta29 validation