X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 19.0
Details PEG3000, Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.9 α = 90
b = 59.01 β = 90
c = 63.83 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-03-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97 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
2.35 50 97.7 0.039 -- -- -- 13364 13340 0.0 0.0 --
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)
2.35 2.43 79.4 0.404 -- 2.3 -- --

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 2.356 50.0 -- 0.0 12707 12707 657 99.01 0.24166 0.24166 0.23869 0.30034 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 2.356 2.417 -- 56 787 0.306 0.339 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.043
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.62
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.042
r_scbond_it 2.939
r_mcangle_it 2.154
r_mcbond_it 1.175
r_symmetry_hbond_refined 0.282
r_symmetry_vdw_other 0.348
r_symmetry_vdw_refined 0.408
r_xyhbond_nbd_other 0.152
r_xyhbond_nbd_refined 0.212
r_bond_refined_d 0.026
r_bond_other_d 0.001
r_angle_refined_deg 2.611
r_angle_other_deg 1.088
r_dihedral_angle_1_deg 6.582
r_dihedral_angle_3_deg 22.235
r_chiral_restr 0.151
r_gen_planes_refined 0.01
r_gen_planes_other 0.003
r_nbd_refined 0.297
r_nbd_other 0.255
r_nbtor_other 0.029
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2087
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 20

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement