3ERB

The Crystal Structure of C2b, a Fragment of Complement Component C2 produced during C3-convertase Formation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OK5	PDB ENTRY 2OK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	18% PEG 3350, 0.22M Sodium Chloride, 0.02M Betaine Hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.06	α = 90
b = 60.06	β = 90
c = 61.687	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	40	100	0.033	21	4.36		23095

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)
	1.8	1.86	100		0.237	5.1	4.15

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OK5	1.8	21.52	21882	1182	99.9	0.21552	0.2142	0.23963	RANDOM	23.257

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]
0.22	0.11		0.22		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.163
r_dihedral_angle_4_deg	16.708
r_dihedral_angle_3_deg	12.198
r_dihedral_angle_1_deg	6.3
r_scangle_it	3.341
r_scbond_it	2.07
r_angle_refined_deg	1.243
r_mcangle_it	1.157
r_mcbond_it	0.813
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.163
r_dihedral_angle_4_deg	16.708
r_dihedral_angle_3_deg	12.198
r_dihedral_angle_1_deg	6.3
r_scangle_it	3.341
r_scbond_it	2.07
r_angle_refined_deg	1.243
r_mcangle_it	1.157
r_mcbond_it	0.813
r_nbtor_refined	0.301
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1415
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.