5D72 | pdb_00005d72

Crystal structure of MOR04252, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 30 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.822	α = 90
b = 97.853	β = 90
c = 192.667	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	PIXEL	DECTRIS PILATUS 6M		2011-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.6	96.22	98	0.075	16.74	5.6		42619

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	2.6	2.77	98		0.715		5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	96.22	40852	897	97.96	0.23231	0.23155	0.23	0.26636	0.27	RANDOM	67.877

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]
-5.43			9.97		-4.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.99
r_dihedral_angle_4_deg	17.505
r_dihedral_angle_3_deg	12.504
r_dihedral_angle_1_deg	6.051
r_scangle_it	3.048
r_scbond_it	2.174
r_mcangle_it	1.512
r_angle_refined_deg	1.146
r_mcbond_it	1.141
r_angle_other_deg	0.884
r_mcbond_other	0.195
r_nbtor_refined	0.154
r_nbd_refined	0.151
r_nbd_other	0.135
r_symmetry_vdw_refined	0.134
r_symmetry_vdw_other	0.103
r_xyhbond_nbd_refined	0.093
r_symmetry_hbond_refined	0.09
r_nbtor_other	0.072
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8096
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
MOLREP	phasing