3Q1Y | pdb_00003q1y

Allosteric regulation by Lysine residue: A novel anion-hole formation in the ribokinase family

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	0.2M MgCl2,200mMCsCl, 20% PEG 3350 0.1M Bis-Tris pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.912	α = 90
b = 44.717	β = 113.48
c = 87.955	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	CCD	ADSC QUANTUM 315	mirrors	2010-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9792	NSLS	X25

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	2.05	50	99.2	0.087	6.7	13.7	20195	20195

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)
	2.05	2.12	94		0.294	10.1	5.5	1901

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3HIC	2.03	50	19156	20154	998	97.51	0.1899	0.1879	0.19	0.2281	0.19	RANDOM	23.675

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]
0.11		0.05	0.56		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.039
r_dihedral_angle_4_deg	18.802
r_dihedral_angle_3_deg	13.332
r_dihedral_angle_1_deg	5.784
r_scangle_it	2.953
r_scbond_it	1.712
r_angle_refined_deg	1.088
r_mcangle_it	1.074
r_mcbond_it	0.556
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.039
r_dihedral_angle_4_deg	18.802
r_dihedral_angle_3_deg	13.332
r_dihedral_angle_1_deg	5.784
r_scangle_it	2.953
r_scbond_it	1.712
r_angle_refined_deg	1.088
r_mcangle_it	1.074
r_mcbond_it	0.556
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2357
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
HKL-2000	data scaling
MOLREP	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.