X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 6
Temperature 277.0
Details crystal 1: 20% PEG-6000, 0.1M MES pH 6.0, 1M LiCl, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Method Vapor Diffusion Sitting Drop Nanodrop
pH 6.6
Temperature 277.0
Details crystal 2: 0.2M ammonium formate, 20% PEG-3350, pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.17 α = 90
b = 45.17 β = 90
c = 177.2 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 flat mirror 2001-06-03
CCD ADSC QUANTUM 315 flat mirror 2002-12-12
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator MAD
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97932, 0.90497 SSRL BL11-1

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
1.83 31.63 99.0 -- 0.072 -- 3.2 16963 16963 -- -- 32.45
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)
1.83 1.88 90.6 -- 0.62 1.7 3.1 1130

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 1.87 31.43 -- -- -- 15161 813 99.41 -- 0.19435 0.19113 0.25495 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 1.87 1.919 -- 65 1069 0.339 0.372 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 32.331
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.34
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.018
r_dihedral_angle_2_deg 32.217
r_symmetry_vdw_other 0.253
r_dihedral_angle_3_deg 13.825
r_angle_refined_deg 1.549
r_nbd_refined 0.208
r_symmetry_vdw_refined 0.106
r_bond_other_d 0.002
r_angle_other_deg 0.882
r_chiral_restr 0.1
r_scbond_it 2.123
r_dihedral_angle_4_deg 8.069
r_xyhbond_nbd_refined 0.222
r_dihedral_angle_1_deg 5.331
r_mcbond_it 0.799
r_nbtor_other 0.085
r_scangle_it 3.409
r_mcangle_it 1.372
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.115
r_gen_planes_other 0.002
r_nbd_other 0.233
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1124
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 214

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 4.2)
SOLVE phasing
RESOLVE model building
REFMAC refinement
CCP4 data scaling version: (SCALA)
RESOLVE phasing