3C9Q | pdb_00003c9q

Crystal structure of the uncharacterized human protein C8orf32 with bound peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			291	Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 M Ammonium sulfate, 0.10 M MES pH 6.0). Cryoprotected in four stages with well solution using 0 to 25 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.322	α = 90
b = 64.039	β = 90
c = 113.66	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	2008-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		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	1.498	32.857	99.5	0.105	12.075	12.2		40943

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	1.498	1.53	95.9		0.543	2.526	6.9	2566

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	SAD	THROUGHOUT	1.5	32.857	40794	2049	99.4	0.162	0.161	0.179	0.18	0.1923	RANDOM	20.35

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]
0.013			0.122		-0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.494
r_dihedral_angle_4_deg	13.371
r_dihedral_angle_3_deg	13.128
r_dihedral_angle_1_deg	6.586
r_scangle_it	5.689
r_scbond_it	4.051
r_mcangle_it	2.64
r_mcbond_it	1.79
r_angle_refined_deg	1.545
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.266
r_symmetry_hbond_refined	0.209
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.113
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1606
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	49

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
SHELXL-97	phasing