Experiment: 3KDO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GEH	PDB ENTRY 1GEH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1M Acetate, 90mM CaCl2, 5% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.481	α = 90
b = 246.573	β = 104.73
c = 134.83	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX225HE		2009-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.36	50	99.6	0.082	13.1			249468

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.36	2.4	99.2		0.389	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GEH	2.36	38.46	236721	12530	99.38	0.22111	0.21886	0.21	0.2638	0.25	RANDOM	31.605

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]
0.54		-2.52	-2.1		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.139
r_dihedral_angle_4_deg	13.734
r_dihedral_angle_3_deg	11.065
r_dihedral_angle_1_deg	3.968
r_scangle_it	0.685
r_angle_refined_deg	0.589
r_scbond_it	0.392
r_mcangle_it	0.379
r_mcbond_it	0.204
r_chiral_restr	0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.139
r_dihedral_angle_4_deg	13.734
r_dihedral_angle_3_deg	11.065
r_dihedral_angle_1_deg	3.968
r_scangle_it	0.685
r_angle_refined_deg	0.589
r_scbond_it	0.392
r_mcangle_it	0.379
r_mcbond_it	0.204
r_chiral_restr	0.042
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34034
Nucleic Acid Atoms
Solvent Atoms	1811
Heterogen Atoms	220

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.