2PMF | pdb_00002pmf

The crystal structure of a human glycyl-tRNA synthetase mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		The native T.thermophilus GlyRS structure

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.412	α = 90
b = 91.412	β = 90
c = 246.814	γ = 90

Symmetry
Space Group	P 43 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		CCD	MARMOSAIC 325 mm CCD		2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.9795	SSRL	BL9-1

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	2.85	50	99.1	0.066	15	13.8		25080

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	2.85	2.95	98.5		0.37		14	2419

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	The native T.thermophilus GlyRS structure	2.85	29.24	24999	1272	98.86	0.233	0.231	0.22	0.271	0.26	RANDOM	60.094

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]
-0.05			-0.05		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.665
r_dihedral_angle_3_deg	15.962
r_dihedral_angle_4_deg	14.902
r_mcangle_it	7.074
r_dihedral_angle_1_deg	6.719
r_scangle_it	4.904
r_mcbond_it	4.783
r_scbond_it	3.341
r_angle_refined_deg	0.847
r_symmetry_hbond_refined	0.335
r_nbtor_refined	0.326
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.199
r_chiral_restr	0.078
r_bond_refined_d	0.003
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4144
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction