X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details K/Na-Phosphate, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.55 α = 90
b = 87.65 β = 90
c = 45.12 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Flat mirror (vertical focusing) 2000-02-13
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.970 SSRL BL9-1

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
1.35 30 98.9 -- 0.053 -- 3.4 -- 117515 0.0 0.0 16.5
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)
1.35 1.37 95.3 -- 0.813 1.13 2.5 5606

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 1.35 18.35 0.0 0.0 109986 104434 5552 93.64 -- 0.15023 0.14949 0.1639 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 1.35 1.385 -- 357 6364 0.261 0.282 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 9.96
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.587
r_nbtor_other 0.566
r_nbd_other 0.201
r_nbd_refined 0.218
r_gen_planes_other 0.002
r_gen_planes_refined 0.007
r_chiral_restr 0.166
r_dihedral_angle_2_deg 16.934
r_dihedral_angle_1_deg 5.638
r_angle_other_deg 1.19
r_angle_refined_deg 1.608
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.17
r_symmetry_vdw_refined 0.176
r_symmetry_vdw_other 0.196
r_symmetry_hbond_refined 0.222
r_symmetry_hbond_other 0.128
r_mcbond_it 1.124
r_mcangle_it 1.691
r_scbond_it 2.755
r_scangle_it 4.043
r_rigid_bond_restr 1.163
r_sphericity_free 20.989
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3119
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 387

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection