X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 3350, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.91 α = 90
b = 58.41 β = 90
c = 149.62 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2006-04-16
CCD ADSC QUANTUM 315 -- 2006-03-16
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.97960 NSLS X29A
SYNCHROTRON NSLS BEAMLINE X25 1.10000 NSLS X25

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
2.15 50 99.6 0.116 0.061 -- 6.4 23284 13258 1.0 1.0 40.8
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)
2.15 2.23 100.0 0.739 -- -- 6.7 2333

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 2.16 46.03 -- 0.0 12567 12567 691 56.78 0.219 0.219 0.217 0.271 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 2.16 2.21 -- 1 49 0.128 0.182 -- 2.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.805
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.25
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.174
r_dihedral_angle_4_deg 25.756
r_dihedral_angle_3_deg 17.14
r_symmetry_vdw_refined 0.267
r_nbd_refined 0.256
r_nbtor_refined 0.316
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 43.814
r_chiral_restr 0.105
r_symmetry_hbond_refined 0.179
r_dihedral_angle_1_deg 5.566
r_gen_planes_refined 0.005
r_angle_refined_deg 1.611
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2046
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 304

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
DM phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
HKL-2000 data collection
HKL-2000 data reduction