X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.8
Temperature 293.0
Details 50% (v/v) PEG-200, 0.1M Tris pH 7.0, pH 6.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 6.80

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.41 α = 115.73
b = 79.96 β = 97.57
c = 89.43 γ = 110.44
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2002-05-19
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL MONOCHROMATOR MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9184, 0.9794, 0.9792 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
2.85 76.7 96.4 -- 0.075 -- 4.1 -- 38502 -- 0.0 19.36
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)
2.85 2.95 96.1 -- 0.232 2.2 3.8 --

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 2.85 24.99 -- -- -- 36521 1938 96.6 -- -- 0.234 0.274 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 2.85 2.92 -- 162 2704 0.265 0.331 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.307
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] -0.71
Anisotropic B[1][3] -0.4
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.01
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.03
r_nbd_other 0.248
r_nbd_refined 0.271
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.095
r_dihedral_angle_2_deg 19.291
r_dihedral_angle_1_deg 4.139
r_angle_other_deg 0.937
r_angle_refined_deg 1.676
r_bond_other_d 0.003
r_bond_refined_d 0.02
r_xyhbond_nbd_refined 0.231
r_xyhbond_nbd_other 0.148
r_symmetry_vdw_refined 0.511
r_symmetry_vdw_other 0.474
r_symmetry_hbond_refined 0.496
r_symmetry_hbond_other 0.395
r_mcbond_it 1.285
r_mcangle_it 2.291
r_scbond_it 1.069
r_scangle_it 1.823
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11068
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 107

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CCP4, SOLVE, RESOLVE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
RESOLVE model building
SOLVE model building
CCP4 model building
CCP4 data reduction
SCALA data reduction
MOSFLM data collection