X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 294.0
Details PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.47 α = 89.98
b = 111.12 β = 101.6
c = 67.91 γ = 89.9
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001-02-08
Diffraction Radiation
Monochromator Protocol
Single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.97 SSRL BL9-1

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
1.7 20 97.0 0.053 0.053 -- 2.22 121277 117639 -3.0 -3.0 28.1
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)
1.7 1.73 95.0 0.357 0.357 2.3 2.0 5780

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
MOLECULAR REPLACEMENT 1.7 19.69 -- -3.0 -- 105810 11826 97.12 0.17174 0.1717 0.16537 0.23002 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 1.7 1.744 5780 820 7574 0.222 0.28 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.342
Anisotropic B[1][1] -0.89
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] -0.17
Anisotropic B[2][2] 1.57
Anisotropic B[2][3] -0.08
Anisotropic B[3][3] -0.75
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.449
r_symmetry_vdw_other 0.264
r_mcbond_it 2.328
r_nbd_other 0.207
r_bond_other_d 0.0
r_dihedral_angle_1_deg 5.359
r_symmetry_vdw_refined 0.269
r_scbond_it 2.688
r_bond_refined_d 0.019
r_angle_other_deg 1.009
r_chiral_restr 0.146
r_scangle_it 4.07
r_gen_planes_other 0.009
r_dihedral_angle_3_deg 18.126
r_gen_planes_refined 0.013
r_symmetry_hbond_refined 0.27
r_nbd_refined 0.233
r_xyhbond_nbd_other 0.15
r_xyhbond_nbd_refined 0.215
r_mcangle_it 3.509
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9476
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1496

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
X-PLOR model building
REFMAC refinement version: 5.0
X-PLOR phasing