X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.1
Temperature 277.0
Details NANODROP, 0.2M Sodium fluoride, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.85 α = 90
b = 82.19 β = 91.37
c = 89.34 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-06-03
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97901, 0.97926 SSRL BL11-1

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
1.6 28 98.7 0.045 -- -- 3.28 -- 101945 -- -3.0 18.5
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)
1.6 1.66 94.5 0.314 -- 2.2 -- --

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 1.6 27.995 -- 0.0 -- 101918 5090 99.4 -- 0.155 0.154 0.18 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 1.6 1.641 -- 361 6844 0.221 0.257 -- 95.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.803
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.75
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.199
r_scbond_it 4.746
r_mcangle_it 2.642
r_xyhbond_nbd_refined 0.164
r_symmetry_vdw_refined 0.179
r_gen_planes_other 0.001
r_nbtor_refined 0.169
r_nbd_other 0.21
r_dihedral_angle_3_deg 12.784
r_dihedral_angle_2_deg 32.953
r_dihedral_angle_4_deg 19.97
r_nbtor_other 0.087
r_symmetry_vdw_other 0.256
r_angle_refined_deg 1.624
r_bond_refined_d 0.017
r_gen_planes_refined 0.007
r_nbd_refined 0.224
r_bond_other_d 0.002
r_chiral_restr 0.103
r_dihedral_angle_1_deg 5.614
r_mcbond_other 0.548
r_scangle_it 6.736
r_symmetry_hbond_refined 0.197
r_xyhbond_nbd_other 0.117
r_angle_other_deg 1.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5505
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 916

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.000
MAR345 data collection version: CCD
XDS data reduction