5MTH | pdb_00005mth

Structure of DC8E8 Fab at pH 6.5 crystallized in spacegroup P21

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OZ4	pdbid 4OZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.45	α = 90
b = 111.77	β = 90.56
c = 95.64	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD		2008-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9999	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.73	38.86	98	0.211	7.98	5.6		88801			24.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76	81.3		3.86	0.108	0.4	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdbid 4OZ4	1.73	38.86	84371	4429	95.27	0.1876	0.1851	0.1675	0.2355	0.2054	RANDOM	29.008

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]
-0.39		7.16	2.45		-2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.883
r_dihedral_angle_4_deg	15.917
r_dihedral_angle_3_deg	13.738
r_dihedral_angle_1_deg	7.405
r_angle_refined_deg	1.898
r_angle_other_deg	1.051
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6721
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	112

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing