2QYA | pdb_00002qya

Crystal structure of an uncharacterized conserved protein from Methanopyrus kandleri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100mM Bis-Tris pH 6.5, 25% PEG 3350, 200mM Lithium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.252	α = 90
b = 49.386	β = 102.75
c = 104.211	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm		2007-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.17	101.64	98.7	0.109	0.109	11.5	3.9	29333	28952			34.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.17	2.29	97.3		0.573	0.573	1.7	3.8	4094

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.17	20	28907	28907	1474	98.63	0.237	0.234	0.2357	0.291	0.2918	RANDOM	51.455

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]
-0.7		-0.58	1.01		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.22
r_dihedral_angle_3_deg	18.524
r_dihedral_angle_4_deg	16.876
r_dihedral_angle_1_deg	6.16
r_scangle_it	3.575
r_scbond_it	2.187
r_mcangle_it	1.58
r_angle_refined_deg	1.575
r_mcbond_it	0.924
r_nbtor_refined	0.303
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.203
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3539
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building