7MLH | pdb_00007mlh

Crystal structure of human IgE (2F10) in complex with Der p 2.0103

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KTJ	1KTJ, 6OY4
experimental model	PDB	6OY4	1KTJ, 6OY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	293	Index A1, Salt: None; Buffer: 0.1M Citric acid pH 3.5; Precipitant: 2.0M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.776	α = 90
b = 231.458	β = 94.338
c = 51.791	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	PIXEL	DECTRIS EIGER2 XE 16M		2020-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.097	40	96.6	0.097	0.097	0.113	0.058	0.987	16.9	3.6		68319

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	86.3		0.428	0.428	0.509	0.269	0.824	1.9	3.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1KTJ, 6OY4	2.1	38.606	68207	3560	96.362	0.212	0.2104	0.22	0.2466	0.25	42.213

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]
-0.086		-1.146	-0.582		0.832

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.974
r_dihedral_angle_3_deg	12.834
r_dihedral_angle_4_deg	11.995
r_dihedral_angle_1_deg	6.009
r_lrange_it	5.94
r_lrange_other	5.861
r_scangle_it	3.133
r_scangle_other	2.93
r_mcangle_it	2.464
r_mcangle_other	2.464
r_angle_other_deg	2.37
r_scbond_it	2.008
r_scbond_other	1.804
r_angle_refined_deg	1.54
r_mcbond_it	1.513
r_mcbond_other	1.512
r_nbd_other	0.302
r_symmetry_xyhbond_nbd_refined	0.271
r_symmetry_nbd_other	0.223
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.184
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.153
r_ncsr_local_group_3	0.123
r_ncsr_local_group_1	0.119
r_ncsr_local_group_2	0.105
r_chiral_restr	0.094
r_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.036
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8267
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing