X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.8
Temperature 277.0
Details PEG 8000, sodium chloride, sodium acetate, sodium citrate buffer, pH 6.8, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.07 α = 90
b = 157.17 β = 97.44
c = 100.18 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 mirror 1999-08-26
Diffraction Radiation
Monochromator Protocol
Si 220 Double Crystal Si 111 Double Crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97927, 0.9393, 0.979 APS 19-ID

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
1.8 75 94.2 0.083 0.083 -- 4.5 229086 229086 0.0 1.0 --
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)
1.8 1.9 75.0 0.527 0.527 2.4 3.5 26449

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 1.8 100.0 -1.0 -1.0 224262 224262 4812 94.12 0.15844 0.15276 0.15193 0.19258 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 1.8 1.847 25768 309 11790 0.251 0.256 -- 75.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Separate TLS groups for each subunit. Individual isotropic temperature factors for all atoms. Overall anisotropic scaling.
Mean Isotropic B 22.888
Anisotropic B[1][1] 0.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.37
Anisotropic B[2][2] 0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.83
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.085
r_nbd_other 0.237
r_nbd_refined 0.212
r_gen_planes_other 0.002
r_gen_planes_refined 0.006
r_chiral_restr 0.092
r_dihedral_angle_2_deg 13.928
r_dihedral_angle_1_deg 5.983
r_angle_other_deg 0.88
r_angle_refined_deg 1.548
r_bond_other_d 0.002
r_bond_refined_d 0.017
r_xyhbond_nbd_refined 0.182
r_symmetry_vdw_refined 0.128
r_symmetry_vdw_other 0.255
r_symmetry_hbond_refined 0.224
r_mcbond_it 0.791
r_mcangle_it 1.403
r_scbond_it 2.31
r_scangle_it 3.715
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.12
Luzzati ESD (R-Free Set) 0.115
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19602
Nucleic Acid Atoms 0
Heterogen Atoms 110
Solvent Atoms 2776

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHAKE-N-BAKE, SHARP Structure Solution
REFMAC 5.1.995 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
SHARP model building
SNB model building
SCALA data reduction
MOSFLM data collection