Experiment: 3ICR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		3 wavelength MAD structure deteremined on Selenomethionine-containing CoADR-RHD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	288	8-16% PEG 8000, 2% 2-methyl-2,4-pentanediol, 0.2M potassium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.48	α = 90
b = 110.47	β = 101.69
c = 79.99	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	RIGAKU SATURN 92	Confocal Blue Max-Flux		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	42.56	99.3	0.097	33.6		66890	66422

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.154	92.5		0.302	7.5		61873

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	3 wavelength MAD structure deteremined on Selenomethionine-containing CoADR-RHD	2.1	42.56	62945	3353	99.03	0.17594	0.17366	0.21833	RANDOM	23.417

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]
0.05		0.06	-0.09		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.288
r_dihedral_angle_4_deg	19.836
r_dihedral_angle_3_deg	14.042
r_dihedral_angle_1_deg	5.684
r_scangle_it	2.717
r_scbond_it	1.81
r_angle_refined_deg	1.268
r_mcangle_it	1.045
r_mcbond_it	0.794
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.288
r_dihedral_angle_4_deg	19.836
r_dihedral_angle_3_deg	14.042
r_dihedral_angle_1_deg	5.684
r_scangle_it	2.717
r_scbond_it	1.81
r_angle_refined_deg	1.268
r_mcangle_it	1.045
r_mcbond_it	0.794
r_nbtor_refined	0.304
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.187
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8596
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	202

Software

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

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.