10DA | pdb_000010da

Crystal structure of Pyrobaculum islandicum L7Ae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CZW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	303	Crystals were grown by vapor diffusion in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 at 303 K. Crystals were cryo-protected in 100 mM Tris-bicine, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 22.5% (v/v) MPD, 30 mM MgCl2, 30 mM CaCl2 and flash frozen with liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.852	α = 87.134
b = 60	β = 75.531
c = 60.71	γ = 84.241

Symmetry
Space Group	P 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	RAYONIX MX-300	Mirrors	2016-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.998	19.89	70.9	0.045	0.027	0.998	14.3	3.9		203846

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.998	1.07	17.6		0.922	0.548	0.602	1.3	3.8

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	0.998	19.89	203839	9969	70.984	0.137	0.1363	0.1352	0.151	0.1495	11.334

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]
-0.665	0.714	0.105	-0.625	-0.666	1.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.717
r_dihedral_angle_3_deg	11.234
r_lrange_it	11.082
r_lrange_other	11.081
r_dihedral_angle_2_deg	7.093
r_dihedral_angle_1_deg	5.752
r_scangle_it	5.296
r_scangle_other	5.296
r_mcangle_other	4.163
r_mcangle_it	4.162
r_scbond_it	3.435
r_scbond_other	3.434
r_rigid_bond_restr	2.542
r_mcbond_it	2.541
r_mcbond_other	2.531
r_angle_refined_deg	1.453
r_angle_other_deg	0.497
r_symmetry_nbd_refined	0.244
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.224
r_symmetry_nbd_other	0.188
r_nbd_other	0.172
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.148
r_chiral_restr	0.078
r_symmetry_metal_ion_refined	0.077
r_symmetry_nbtor_other	0.076
r_metal_ion_refined	0.05
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4343
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing