2FC3 | pdb_00002fc3

Crystal structure of the extremely thermostable Aeropyrum pernix L7Ae multifunctional protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XBI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20% PEG 4000, 10% Isopropanol, 100 mM HEPES-KOH, pH 7.5, 1 mM ZnCl2 mixed 1:2 with 500 microMolar L7Ae protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.054	α = 90
b = 49.188	β = 90
c = 65.048	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	RIGAKU SATURN 92	Osmic Confocal Blue Max-Flux	2004-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.54	65.05	81.5	0.025	23.7	2.45	34157	13926		3	17.53

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	1.54	1.6	15.8		0.289	2.3	1.08	1678

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1XBI	1.56	32.44	1	13760	13737	695	99.08	0.177	0.177	0.174	0.19	0.226	0.23	RANDOM	15.807

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]
0.02			-0.56		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.439
r_dihedral_angle_4_deg	15.801
r_sphericity_free	11.286
r_dihedral_angle_3_deg	11.016
r_dihedral_angle_1_deg	5.482
r_scangle_it	4.634
r_scbond_it	3.161
r_sphericity_bonded	3.042
r_rigid_bond_restr	2.132
r_mcangle_it	1.822
r_mcbond_it	1.542
r_angle_refined_deg	1.419
r_angle_other_deg	0.928
r_mcbond_other	0.431
r_symmetry_vdw_other	0.363
r_nbd_refined	0.21
r_nbd_other	0.193
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.118
r_chiral_restr	0.085
r_nbtor_other	0.082
r_symmetry_vdw_refined	0.049
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	957
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling