7CNU | pdb_00007cnu

Crystal structure of DLC2 in complex with BMF peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XQQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium chloride 0.1 M HEPES 7.0 20 % w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.243	α = 90
b = 38.701	β = 99.87
c = 44.699	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS3 S 6M		2017-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.98	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	41.93	98.98	0.997	11.78	5.6		19215

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.951

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 (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	2XQQ	2	41.93	17305	1923	99.27	0.19645	0.19325	0.2	0.22565	0.24	RANDOM	48.342

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]
-1.74		1.42	3.19		-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.988
r_dihedral_angle_3_deg	15.574
r_dihedral_angle_4_deg	8.908
r_long_range_B_refined	8.389
r_long_range_B_other	8.38
r_scangle_other	6.603
r_dihedral_angle_1_deg	6.515
r_scbond_it	4.389
r_scbond_other	4.389
r_mcangle_it	3.472
r_mcangle_other	3.438
r_mcbond_it	2.66
r_mcbond_other	2.631
r_angle_refined_deg	1.436
r_angle_other_deg	1.073
r_chiral_restr	0.095
r_bond_refined_d	0.012
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	2158
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing