2RLD | pdb_00002rld

CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM S23 RIBOSOMAL PROTEIN FAMILY (BT_0352) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.70 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	277	NANODROP, 0.2M CaCl2, 20.0% PEG 3350, no Buffer pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.238	α = 90
b = 83.823	β = 97.42
c = 63.923	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	ADSC QUANTUM 315		2007-10-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9798, 0.9537, 0.9796	ALS	8.2.2

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	1.7	29.643	96.2	0.053	0.053	9.1	2		63158			20.65

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)
1	1.7	1.74	88.2		0.441	0.441	1.7	1.8	4288

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.7	29.643	63130	3216	95.92	0.165	0.163	0.17	0.201	0.21	RANDOM	17.012

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]
0.87		0.19	-0.29		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.276
r_dihedral_angle_3_deg	12.39
r_dihedral_angle_4_deg	11.604
r_scangle_it	6.586
r_scbond_it	4.41
r_dihedral_angle_1_deg	4.356
r_mcangle_it	2.204
r_mcbond_it	1.661
r_angle_refined_deg	1.196
r_angle_other_deg	0.899
r_mcbond_other	0.614
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.183
r_nbd_other	0.178
r_symmetry_vdw_other	0.148
r_nbtor_other	0.084
r_chiral_restr	0.075
r_metal_ion_refined	0.071
r_symmetry_metal_ion_refined	0.049
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4478
Nucleic Acid Atoms
Solvent Atoms	518
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SOLVE	phasing