8CN6 | pdb_00008cn6

CD59 in complex with CP-06 peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.01 M ZnCl2, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.94	α = 90
b = 85.88	β = 90.03
c = 96.57	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 16M		2019-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.43	48.332	99.1	0.102	0.122	0.066	0.99	7	3.4		18920			78.67

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.43	2.47	99.5		0.23	0.272	0.143	0.29	0.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.43	48.332	18901	969	98.948	0.239	0.2353	0.2344	0.2983	0.2985	78.563

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]
-1.882		0.344	1.587		0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.707
r_dihedral_angle_3_deg	17.896
r_lrange_it	14.724
r_lrange_other	14.724
r_dihedral_angle_6_deg	13.729
r_scangle_it	12.077
r_scangle_other	12.075
r_mcangle_it	10.109
r_mcangle_other	10.108
r_dihedral_angle_other_2_deg	9.328
r_scbond_it	8.661
r_scbond_other	8.661
r_dihedral_angle_1_deg	8.647
r_mcbond_it	7.441
r_mcbond_other	7.44
r_angle_refined_deg	2.777
r_angle_other_deg	1.061
r_symmetry_xyhbond_nbd_refined	0.296
r_metal_ion_refined	0.279
r_nbd_refined	0.254
r_nbd_other	0.241
r_xyhbond_nbd_refined	0.236
r_symmetry_nbd_other	0.224
r_symmetry_nbd_refined	0.223
r_nbtor_refined	0.206
r_ncsr_local_group_5	0.137
r_chiral_restr	0.136
r_ncsr_local_group_13	0.135
r_ncsr_local_group_2	0.131
r_ncsr_local_group_14	0.128
r_ncsr_local_group_4	0.124
r_ncsr_local_group_9	0.124
r_ncsr_local_group_11	0.123
r_ncsr_local_group_10	0.118
r_ncsr_local_group_6	0.115
r_ncsr_local_group_3	0.111
r_ncsr_local_group_8	0.11
r_ncsr_local_group_15	0.11
r_ncsr_local_group_1	0.107
r_ncsr_local_group_7	0.104
r_ncsr_local_group_12	0.1
r_symmetry_nbtor_other	0.095
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3691
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	362

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing