3PLS | pdb_00003pls

RON in complex with ligand AMP-PNP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5		20% PEG2K and 2mM MgCl2, pH 7.5, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.631	α = 90
b = 98.631	β = 90
c = 45.297	γ = 90

Symmetry
Space Group	P 41

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	MARMOSAIC 225 mm CCD		2008-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

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	2.24	98.53	89	0.052		4.6		21232

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	2.24	2.3	54.6		0.509		4.3

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		THROUGHOUT	2.24	49.32	20008	1360	94.26	0.2352	0.2313	0.24	0.2897	0.29	RANDOM	52.9698

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]
-3.86			-3.86		7.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.284
r_dihedral_angle_3_deg	17.251
r_dihedral_angle_4_deg	15.285
r_dihedral_angle_1_deg	6.214
r_scangle_it	5.582
r_scbond_it	4.185
r_mcangle_it	2.937
r_mcbond_it	2.431
r_angle_refined_deg	1.278
r_angle_other_deg	0.776
r_mcbond_other	0.494
r_symmetry_vdw_other	0.211
r_nbd_refined	0.195
r_nbd_other	0.181
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.144
r_nbtor_other	0.085
r_chiral_restr	0.074
r_metal_ion_refined	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling