1T2J | pdb_00001t2j

Crystal structure of a Human VH domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ModelArchive	MA-CNZ8J	ENTRY 1HOU that was moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Crystals grew from 3 microlitre hangingdrop formed by mixing 1.5 microlitre of protein:subtilisin mixture (250:1 M ratio) at protein conc. 13.5 mg/ml with 1.5 microlitre of reservoir solution 100mM MES, pH6.5, 10mM ZnSO4, 25% v/v PEG550MME, 4mM DTT and 0.04% v/v NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.336	α = 90
b = 37.965	β = 109.67
c = 37.187	γ = 90

Symmetry
Space Group	C 1 2 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	MARRESEARCH	Rh coated mirror	2003-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.802	EMBL/DESY, HAMBURG	X31

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	1.5	34.922	90.7	0.047	27.69	4.29		15017			16.67

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)
	1.5	1.53	92.9		0.214	7.26	4.1	696

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 1HOU	1.5	20	15144	14358	762	99.89	0.1763	0.15979	0.15787	0.16	0.19652	0.19	RANDOM	21.603

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]
-0.75		-0.54	1.87		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.651
r_scangle_it	3.897
r_scbond_it	3.504
r_mcangle_it	3.229
r_mcbond_it	1.924
r_angle_refined_deg	1.735
r_nbd_refined	0.241
r_symmetry_vdw_refined	0.211
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.11
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	877
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing