3MXV | pdb_00003mxv

Crystal structure of fab fragment of anti-Shh 5E1 chimera

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	292	protein (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volumes of reservoir solution (0.2M Ammonium Sulfate, 20% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.287	α = 90
b = 110.287	β = 90
c = 122.509	γ = 120

Symmetry
Space Group	H 3

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		2008-12-10	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	1.9	50	100	0.07	15.8	3.2	43883	43883		-3	18

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	1.9	1.97	100		0.482	2.3	3.2	4395

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB entry 1FVE	1.9	44.5	-3	43833	43833	4370	99.99	0.18303	0.18303	0.17853	0.18	0.22387	0.22	RANDOM	25.459

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]
0.54	0.27		0.54		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.885
r_dihedral_angle_4_deg	17.397
r_dihedral_angle_3_deg	11.505
r_dihedral_angle_1_deg	6.278
r_scangle_it	4.169
r_mcangle_it	3.32
r_scbond_it	2.834
r_mcbond_it	2.325
r_angle_refined_deg	1.205
r_nbtor_refined	0.298
r_symmetry_hbond_refined	0.204
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3311
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	20

Software

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