3DRY

X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5		0.2 M proline, 100 mM HEPES, 7% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.99	α = 90
b = 106.791	β = 90
c = 110.174	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 K-B GEOMETRY	2006-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97915	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	3.3	50	99.5	0.074	18.14	5.2		20180

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	3.3	3.4	97.6		0.51	1.9	4.8	1151

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3DRX	3.3	20	16774	1913	99.7	0.26018	0.26018	0.25257	0.30791	RANDOM	73.224

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]
-8.94			-4.73		13.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.47
r_dihedral_angle_3_deg	19.233
r_dihedral_angle_4_deg	17.817
r_dihedral_angle_1_deg	6.843
r_angle_refined_deg	1.276
r_angle_other_deg	0.941
r_scangle_it	0.743
r_scbond_it	0.478
r_mcangle_it	0.428
r_mcbond_it	0.373
r_nbd_refined	0.232
r_symmetry_vdw_other	0.213
r_symmetry_hbond_refined	0.21
r_symmetry_vdw_refined	0.196
r_nbd_other	0.19
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.166
r_nbtor_other	0.087
r_xyhbond_nbd_other	0.07
r_chiral_restr	0.066
r_mcbond_other	0.051
r_bond_refined_d	0.012
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6810
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing