1KD1 | pdb_00001kd1

Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JJ2	1JJ2.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.8	292	PEG 6K, KCl, NH4Cl, NaOAc, MgCl2, pH 5.8, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 212.902	α = 90
b = 300.474	β = 90
c = 575.176	γ = 90

Symmetry
Space Group	C 2 2 21

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	CUSTOM-MADE	Si-111, Si-220	2000-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.033	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	50	99.9	0.152	0.152	12.1	7	363802	363802	-3	-3	42.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3	3.11	99.9		0.853	0.853	2.6	5	36147

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JJ2.pdb	3	19.99	357528	333395	3278	91.7	0.22	0.22	0.22	0.22	0.269	RANDOM IDENTICAL TEST set from 1JJ2.pdb	58.7

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]
15.27			-5.73		-9.54

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.7
c_scangle_it	1.93
c_mcangle_it	1.76
c_improper_angle_d	1.59
c_angle_deg	1.4
c_scbond_it	1.21
c_mcbond_it	1.02
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28801
Nucleic Acid Atoms	61617
Solvent Atoms	7876
Heterogen Atoms	293

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing