5MC7 | pdb_00005mc7

Crystal structure of Truncated Human Coatomer Protein Complex, subunit Z1 (CopZ1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	2.2 M DL-Malic acid 0.2 M Na Malonate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.36	α = 90
b = 65.403	β = 96.58
c = 37.273	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 PILATUS 6M	LN2 cooled double crystal monochromator and two horizontal deflecting and one vertical deflecting X-ray mirror	2016-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033200	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.6	56.03	97.3	0.046	0.998	16	3.0246		33495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	95.4		0.37	0.883	2.6	3

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	2HF6	1.6	56.03	31877	1619	97.34	0.21243	0.21041	0.22	0.251	0.26	RANDOM	20.047

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]
-0.48		0.21	-0.09		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.673
r_dihedral_angle_4_deg	17.91
r_dihedral_angle_3_deg	15.804
r_dihedral_angle_1_deg	6.15
r_long_range_B_refined	3.529
r_long_range_B_other	3.511
r_angle_refined_deg	2.569
r_scangle_other	2.366
r_scbond_it	1.573
r_scbond_other	1.573
r_mcangle_other	1.377
r_mcangle_it	1.376
r_angle_other_deg	1.284
r_mcbond_it	0.923
r_mcbond_other	0.913
r_chiral_restr	0.187
r_bond_refined_d	0.03
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2224
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms

Software

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