6FAX

Complex of Human CD40 Ectodomain with Lob 7.4 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U6A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NA
2	VAPOR DIFFUSION, HANGING DROP		293	NA

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.86
2.27	45.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.753	α = 90
b = 158.753	β = 90
c = 93.622	γ = 120

Symmetry
Space Group	P 31 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-F		2015-04-04	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976254	ESRF	ID23-1
2	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.969995	ESRF	ID23-1

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	2.99	52	99.9	0.161	0.998	13.7	13.7		27589

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	2.99	3.18	99.3		0.912	2.4	6.2

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	1U6A	2.99	137.48	26355	1319	99.67	0.18707	0.18482	0.23121	RANDOM	84.715

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]
2.59	1.3		2.59		-8.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.454
r_dihedral_angle_3_deg	20.7
r_dihedral_angle_4_deg	18.582
r_long_range_B_refined	14.058
r_long_range_B_other	14.057
r_scangle_other	11.561
r_dihedral_angle_1_deg	10.747
r_mcangle_it	10.217
r_mcangle_other	10.215
r_scbond_it	8.25
r_scbond_other	8.25
r_mcbond_it	7.148
r_mcbond_other	7.135
r_angle_refined_deg	2.134
r_angle_other_deg	1.154
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
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	4057
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms

Software

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