9SHC | pdb_00009shc

Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	Don't know.

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.365	α = 90
b = 72.888	β = 117.42
c = 78.881	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 210		2002-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	20	93.9	0.085	8.2	3.5		31310

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36			0.382		1.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	20	31310	1561	93.09	0.21	0.2083	0.2161	0.2471	0.2536	39.998

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]
-2.847		-0.929	4.181		-0.241

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.245
r_dihedral_angle_6_deg	11.93
r_dihedral_angle_1_deg	6.066
r_lrange_it	5.231
r_lrange_other	5.229
r_dihedral_angle_2_deg	4.541
r_scangle_it	3.556
r_scangle_other	3.556
r_mcangle_it	3.17
r_mcangle_other	3.17
r_scbond_it	2.035
r_scbond_other	2.035
r_mcbond_it	1.851
r_mcbond_other	1.849
r_angle_refined_deg	1.033
r_angle_other_deg	0.407
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.196
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.106
r_nbd_other	0.095
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.056
r_symmetry_xyhbond_nbd_refined	0.028
r_dihedral_angle_other_2_deg	0.004
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4032
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	31

Software

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