6KO8

Crystal structure of the Cholic acid bound RamR determined with XtaLAB Synergy

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VVY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	298	PEG3350, ammonium sulfate, sodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.69	α = 90
b = 53.897	β = 93.06
c = 44.223	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	RIGAKU HyPic-6000HE		2016-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	22.09	99.6	0.034	0.037	0.015	0.999	16.6	4.6		29492

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	97.9		0.637	0.772	0.424	0.645		3

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	3VVY	1.55	22.09	27959	1533	99.49	0.1491	0.1461	0.2038	RANDOM	35.451

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]
-2.54		0.83	2.16		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.726
r_dihedral_angle_4_deg	18.067
r_dihedral_angle_3_deg	16.19
r_dihedral_angle_1_deg	7.804
r_rigid_bond_restr	4.729
r_angle_refined_deg	1.855
r_angle_other_deg	1.631
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.726
r_dihedral_angle_4_deg	18.067
r_dihedral_angle_3_deg	16.19
r_dihedral_angle_1_deg	7.804
r_rigid_bond_restr	4.729
r_angle_refined_deg	1.855
r_angle_other_deg	1.631
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1447
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction

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 R01GM133198.