2RD7 | pdb_00002rd7

Human Complement Membrane Attack Proteins Share a Common Fold with Bacterial Cytolysins

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Lower resolution model solved by SAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	289	6% PEG 20,000, 0.1 M citric acid, 0.025 M Mg(NO3)2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.553	α = 90
b = 126.087	β = 90
c = 51.887	γ = 90

Symmetry
Space Group	P 21 21 2

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9565	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	50	93.2	0.048	0.048	33.4	4	32462	32462		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.24	84.2		0.4	0.315	2.6	3.1	2876

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Lower resolution model solved by SAD	2.15	34	30735	30735	1616	91.87	0.20827	0.20827	0.20563	0.28	0.26086	0.33	RANDOM	45.718

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]
0.11			-1.59		1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.382
r_dihedral_angle_4_deg	19.409
r_dihedral_angle_3_deg	16.557
r_dihedral_angle_1_deg	7.395
r_scangle_it	3.613
r_scbond_it	2.323
r_mcangle_it	1.705
r_angle_refined_deg	1.63
r_mcbond_it	1.022
r_angle_other_deg	0.886
r_symmetry_vdw_other	0.256
r_mcbond_other	0.227
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.205
r_nbd_other	0.198
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.107
r_nbtor_other	0.091
r_symmetry_hbond_refined	0.081
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_xyhbond_nbd_other
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	3844
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
RESOLVE	phasing
O	model building
CCP4	phasing
MOLREP	phasing
Coot	model building