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 = 38.43 α = 89.99
b = 111.22 β = 101.45
c = 67.78 γ = 89.75
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
1.9 20 98.0 0.04 0.04 -- 2.05 86252 84527 -3.0 -3.0 32.8
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)
1.9 1.93 96.0 0.251 0.251 2.5 1.95 4202

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 1.9 19.69 -- -3.0 84527 84527 8529 97.58 0.16914 0.16914 0.16204 0.23417 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 1.9 1.949 4202 641 5472 0.199 0.29 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 27.376
Anisotropic B[1][1] -1.29
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] -0.46
Anisotropic B[2][2] 1.79
Anisotropic B[2][3] -0.18
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.0
r_angle_refined_deg 2.589
r_bond_refined_d 0.018
r_nbtor_other 0.018
r_scbond_it 2.788
r_symmetry_vdw_other 0.23
r_scangle_it 4.187
r_symmetry_hbond_refined 0.253
r_mcbond_it 2.542
r_dihedral_angle_3_deg 18.99
r_nbd_other 0.21
r_symmetry_vdw_refined 0.247
r_symmetry_hbond_other 0.059
r_nbd_refined 0.234
r_xyhbond_nbd_other 0.165
r_angle_other_deg 1.059
r_gen_planes_other 0.008
r_mcangle_it 3.799
r_chiral_restr 0.156
r_xyhbond_nbd_refined 0.212
r_dihedral_angle_1_deg 5.546
r_gen_planes_refined 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9408
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1123

Software

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