2I9W | pdb_00002i9w

Crystal structure of a sec-c motif containing protein (psyc_2064) from psychrobacter arcticus at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	8.5	277	0.2M MgCl2, 20.0% PEG-8000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.49	α = 90
b = 54.69	β = 90
c = 83.88	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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.94926,0.97939,0.97925	APS	23-ID-D

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	1.75	29.501	93.9	0.056	9.19			19754			27.791

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	1.75	1.81	83.8		0.361	2.2		3015

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	MAD	THROUGHOUT	1.75	29.501	19707	1007	99.23	0.19392	0.192	0.2	0.238	0.24	RANDOM	20.135

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]
1.6			-0.26		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_dihedral_angle_3_deg	13.377
r_dihedral_angle_4_deg	7.59
r_scangle_it	6.423
r_dihedral_angle_1_deg	5.811
r_scbond_it	4.796
r_mcangle_it	2.978
r_mcbond_it	2.096
r_angle_refined_deg	1.522
r_angle_other_deg	0.903
r_mcbond_other	0.505
r_symmetry_vdw_refined	0.289
r_symmetry_vdw_other	0.269
r_nbd_refined	0.235
r_nbd_other	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.087
r_nbtor_other	0.087
r_bond_refined_d	0.015
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	1370
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
SHARP	phasing