2Q7E | pdb_00002q7e

The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	289	100mM Tris 10% PEG2000 MME , pH 7.5, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.124	α = 90
b = 105.124	β = 90
c = 70.314	γ = 120

Symmetry
Space Group	P 64

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	si 111	2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97917	APS	24-ID-C

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	1.8	40	98.75	0.048	48.2	10.6	40633	38485	1	1

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	1.8	1.86	95.7		0.879	2	7.3

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	SIRAS	THROUGHOUT	1.8	34.4	38485	2042	98.75	0.16727	0.16595	0.17	0.19119	0.2	RANDOM	37.263

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]
-0.52	-0.26		-0.52		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.606
r_dihedral_angle_4_deg	13.33
r_dihedral_angle_3_deg	12.782
r_dihedral_angle_1_deg	6.218
r_scangle_it	6.182
r_mcangle_it	4.654
r_scbond_it	4.63
r_mcbond_it	4.138
r_angle_refined_deg	1.297
r_mcbond_other	1.024
r_angle_other_deg	0.842
r_symmetry_vdw_other	0.247
r_nbd_refined	0.209
r_nbd_other	0.191
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.144
r_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2105
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing