Experiment: 3DJW

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	1.35M Sodium Citrate, 0.1M Sodium Hepes, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.411	α = 90
b = 101.411	β = 90
c = 58.522	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	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	3.1	40	99.7	0.101	0.101	4.4	7.5		5897			84.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.27	100		0.556	0.556	3.3	7.8	843

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DF6 chain A	3.1	15	5246	560	99.66	0.24976	0.24504	0.29631	RANDOM	66.857

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.77			-2.77		5.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.124
r_dihedral_angle_3_deg	18.415
r_dihedral_angle_4_deg	12.848
r_dihedral_angle_1_deg	5.505
r_angle_refined_deg	1.065
r_scangle_it	0.935
r_scbond_it	0.564
r_nbtor_refined	0.308
r_mcangle_it	0.279
r_symmetry_vdw_refined	0.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.124
r_dihedral_angle_3_deg	18.415
r_dihedral_angle_4_deg	12.848
r_dihedral_angle_1_deg	5.505
r_angle_refined_deg	1.065
r_scangle_it	0.935
r_scbond_it	0.564
r_nbtor_refined	0.308
r_mcangle_it	0.279
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.17
r_mcbond_it	0.146
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1582
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.