X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 0.1 M HEPES buffer, 22% PEG 3350, 200 mM KSCN, 2.0 mM K2PtCl6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.81 α = 93.17
b = 49.78 β = 94.87
c = 54.96 γ = 102.86
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-11-23
Diffraction Radiation
Monochromator Protocol
Double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.071 EMBL/DESY, HAMBURG X12

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
1.94 54.6 94.2 0.068 -- -- 3.7 29990 29990 0.0 -3.0 --
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)
1.94 2.01 75.0 0.153 -- 4.98 2.8 --

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 1.94 54.6 -- -- 29990 28971 1019 94.08 -- 0.18675 0.18534 0.22665 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 1.94 1.988 -- 62 1631 0.146 0.231 -- 71.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.057
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] -1.09
Anisotropic B[1][3] 2.04
Anisotropic B[2][2] -1.22
Anisotropic B[2][3] -0.17
Anisotropic B[3][3] 1.05
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.422
r_scbond_it 2.512
r_mcangle_it 1.426
r_mcbond_it 0.952
r_gen_planes_refined 0.009
r_chiral_restr 0.13
r_dihedral_angle_4_deg 17.178
r_dihedral_angle_3_deg 15.31
r_dihedral_angle_2_deg 32.693
r_dihedral_angle_1_deg 6.9
r_angle_refined_deg 1.694
r_bond_refined_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3836
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 231

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Auto-Rickshaw MR protocol Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
Auto-Rickshaw version: MR protocol model building
HKL-2000 data collection