3MBX | pdb_00003mbx

Crystal structure of chimeric antibody X836

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q9Q	PDB ENTRY 1Q9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	0.1 M PHOSPHATE-CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE, 10% PEG 3350; CRYO CONDITIONS: MOTHER LIQUOR + 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.93	α = 90
b = 99.84	β = 90
c = 125.33	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	118	CCD	RIGAKU SATURN 944	VARIMAX HF	2007-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	43.5	96.9	0.088	12.6	8	69807	69807		-3	24.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	91.8		0.436	3	4.5	6545

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	PDB ENTRY 1Q9Q	1.6	15	67553	67553	2111	93.9	0.21062	0.21062	0.20993	0.21	0.23204	0.24	RANDOM	28.7

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]
0.07			0.35		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	32.981
r_dihedral_angle_2_deg	32.282
r_scbond_it	29.696
r_dihedral_angle_4_deg	19.204
r_dihedral_angle_3_deg	12.823
r_dihedral_angle_1_deg	6.334
r_mcangle_it	5.562
r_mcbond_it	3.612
r_angle_refined_deg	1.411
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.101
r_symmetry_hbond_refined	0.099
r_bond_refined_d	0.011
r_gen_planes_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3468
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling