Experiment: 3MXW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VHH	PDB entry 1VHH, refined fab

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	protein solution (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volume of well solution (0.2 M lithium sulfate, 100 mM Hepes, pH 7.5, and 22% w/v PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.306	α = 90
b = 90.544	β = 90
c = 111.672	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 210	Single crystal, cylindrically bent, Si(220)	2009-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97740	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.83	50	98.8	0.068	16.4	4.3		54683		-3	19.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.9	90.7		0.464	2.2	2.6	4917

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VHH, refined fab	1.83	47.51	-3	54255	5441	98.86	0.18056	0.18056	0.17639	0.21844	RANDOM	25.797

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]
-0.85			0.54		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.743
r_dihedral_angle_4_deg	15.895
r_dihedral_angle_3_deg	11.538
r_dihedral_angle_1_deg	6.486
r_scangle_it	4.446
r_mcangle_it	3.46
r_scbond_it	3.063
r_mcbond_it	2.596
r_angle_refined_deg	1.255
r_symmetry_hbond_refined	0.362

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.743
r_dihedral_angle_4_deg	15.895
r_dihedral_angle_3_deg	11.538
r_dihedral_angle_1_deg	6.486
r_scangle_it	4.446
r_mcangle_it	3.46
r_scbond_it	3.063
r_mcbond_it	2.596
r_angle_refined_deg	1.255
r_symmetry_hbond_refined	0.362
r_nbtor_refined	0.3
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.183
r_metal_ion_refined	0.15
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4537
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	18

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM133198.