6RS8

X-ray crystal structure of LsAA9B (transition metals soak)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EJA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1M HEPES/MOPS pH 7.5 12.5 %(v/v) MPD (racemic) 12.5 %(w/v) PEG 1000 12.5 %(w/v) PEG 3350 0.02M of each of Na-formate, NH4-acetate, Na-citrate, Na/K-tartrate, Na-oxamate.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.16	α = 90
b = 72.58	β = 90
c = 78.68	γ = 90

Symmetry
Space Group	P 21 21 21

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		2014-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.3499	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.58	40	92.4	0.055	0.999	28.46	8.6		27805

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.62	72.4		0.391	0.826		2.84

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EJA	1.58	39.37	26400	1413	97.45	0.11573	0.11267	0.17312	RANDOM	13.534

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]
0.2			0.21		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.786
r_dihedral_angle_4_deg	12.79
r_sphericity_bonded	12.069
r_dihedral_angle_3_deg	11.464
r_dihedral_angle_1_deg	7.106
r_rigid_bond_restr	4.134
r_long_range_B_refined	3.667
r_long_range_B_other	3.667
r_scangle_other	3.495
r_scbond_it	3.112
r_scbond_other	3.111
r_mcangle_other	2.108
r_mcangle_it	2.093
r_angle_refined_deg	1.828
r_mcbond_it	1.698
r_mcbond_other	1.698
r_angle_other_deg	1.057
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1645
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building