1VMB | pdb_00001vmb

Crystal structure of 30S ribosomal protein S6 (TM0603) from Thermotoga maritima at 1.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	20.0% PEG-3350, 0.1M NaAcetate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.815	α = 90
b = 60.815	β = 90
c = 76.543	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 315	flat mirror	2004-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.7	47.62	96.2	0.073	16.2	5.4		15840			29.25

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)
1	1.7	1.74	73.9		0.391	2.1	2.8	880

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	1lou	1.7	47.62	15000	788	96.32	0.18549	0.18287	0.2	0.23735	0.26	RANDOM	22.517

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]
0.65			0.65		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.345
r_dihedral_angle_4_deg	15.132
r_dihedral_angle_3_deg	12.855
r_dihedral_angle_1_deg	5.767
r_scangle_it	4.071
r_scbond_it	2.832
r_angle_refined_deg	1.643
r_mcangle_it	1.577
r_mcbond_it	1.32
r_angle_other_deg	0.927
r_mcbond_other	0.351
r_symmetry_vdw_other	0.318
r_nbd_refined	0.205
r_nbd_other	0.202
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.106
r_nbtor_other	0.083
r_symmetry_vdw_refined	0.062
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	922
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	8

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling