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 0.0015mL protein solution (100mM Tris/HCl, pH 7.0, 150mM NaCl), 0.0003mL spermidine, 0.0012mL reservoir solution (20% PEG 550 MME, 0.1M HEPES, pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.59 α = 90
b = 116.59 β = 90
c = 174.33 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2008-06-20
Diffraction Radiation
Monochromator Protocol
silicon (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.0707 SLS X10SA

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
1.85 50 98.8 0.124 0.124 -- 4.4 101118 99904 0.0 0.0 18.9
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)
1.85 1.9 94.1 0.574 0.574 1.5 3.0 9481

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 1.85 15.0 0.0 0.0 97046 95678 5028 98.59 -- 0.18751 0.1863 0.2106 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 1.852 1.899 -- 306 6348 0.249 0.278 -- 91.15
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 18.911
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.91
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.118
r_bond_refined_d 0.01
r_angle_refined_deg 1.211
r_symmetry_hbond_refined 0.191
r_gen_planes_refined 0.004
r_mcbond_it 0.686
r_dihedral_angle_1_deg 5.772
r_scangle_it 3.145
r_nbd_refined 0.196
r_nbtor_refined 0.302
r_dihedral_angle_4_deg 19.997
r_mcangle_it 1.075
r_chiral_restr 0.088
r_dihedral_angle_3_deg 13.86
r_symmetry_vdw_refined 0.197
r_scbond_it 1.941
r_dihedral_angle_2_deg 38.553
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.12
Luzzati ESD (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6812
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 434

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
SCALEPACK data scaling