X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.6
Temperature 277.0
Details 0.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.74 α = 90
b = 108.95 β = 90
c = 207.64 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-10
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- 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
2.9 29.77 99.9 0.243 0.243 -- 3.7 -- 40426 -- -- 42.549
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)
2.9 2.98 100.0 0.749 0.749 1.0 3.7 2934

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
MR 2.9 29.775 -- 0.0 -- 40367 2022 99.86 -- 0.225 0.223 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 2.9 2.975 -- 142 2788 0.313 0.372 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.943
Anisotropic B[1][1] -1.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.05
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_bond_other_d 0.003
r_mcangle_it 0.526
r_symmetry_vdw_other 0.123
r_dihedral_angle_4_deg 8.808
r_dihedral_angle_3_deg 9.036
r_chiral_restr 0.065
r_scbond_it 0.26
r_dihedral_angle_1_deg 2.167
r_nbd_refined 0.161
r_bond_refined_d 0.011
r_scangle_it 0.397
r_mcbond_it 0.318
r_nbtor_other 0.084
r_xyhbond_nbd_other 0.004
r_nbtor_refined 0.164
r_symmetry_vdw_refined 0.079
r_gen_planes_refined 0.005
r_nbd_other 0.139
r_xyhbond_nbd_refined 0.157
r_angle_other_deg 0.879
r_symmetry_hbond_refined 0.17
r_dihedral_angle_2_deg 24.6
r_mcbond_other 0.061
r_angle_refined_deg 1.065
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12883
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
PHASER phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction