4HAF | pdb_00004haf

Crystal structure of fc-fragment of human IgG2 antibody (primitive crystal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AVE	PDB entry 3ave

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES, 9% PEG 4000, 0.2 M AMMONIUM CHLORIDE, 5% MPD CRYO CONDITIONS: 0.1 M MES, 12% PEG 4000, 0.2 M AMMONIUM CHLORIDE, 20% PEG 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.5	α = 90
b = 75.17	β = 90
c = 146.01	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	CCD	RIGAKU SATURN 944	VARIMAX HF	2010-03-19	M	SINGLE WAVELENGTH

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

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	2.04	27.7	98.7	0.085	18.7	6.7	35162	35162	-3	-3	26.8

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	2.04	2.09	83.9		0.357	3.1	2.6

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 3ave	2.04	15	34097	34097	970	96	0.20041	0.20041	0.19902	0.2	0.24819	0.25	RANDOM	35.1

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]
-0.69			-0.24		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.759
r_scangle_it	30.36
r_scbond_it	27.505
r_dihedral_angle_4_deg	15.524
r_dihedral_angle_3_deg	14.008
r_dihedral_angle_1_deg	5.794
r_mcangle_it	5.104
r_mcbond_it	3.233
r_angle_refined_deg	1.189
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.759
r_scangle_it	30.36
r_scbond_it	27.505
r_dihedral_angle_4_deg	15.524
r_dihedral_angle_3_deg	14.008
r_dihedral_angle_1_deg	5.794
r_mcangle_it	5.104
r_mcbond_it	3.233
r_angle_refined_deg	1.189
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3183
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	99

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.